This is going to get unwieldy, but I want to respond point by point:
First, Vanessa’s ID is left behind in her Arms room. AR’s Arms Room is in a neighboring building. Wouldn’t she have needed her ID to get access to the building AR’s Arms Room is in? Either she would have to swipe her ID to open doors or show it to a guard. I can’t imagine a soldier wandering around in secure buildings without an ID and I can’t imagine doors are left unlocked for anyone to go in and out. I also can't imagine she carries a set of keys for various doors. Maybe I’m wrong about that, but it seems like an ID should be required. When I worked corporate jobs with far less important stuff going on, our IDs were either hanging around our necks or clipped to our waists. And we had to use them to open doors into office spaces and to get off elevators.
Most buildings on military installations are not necessarily access-controlled unless they have a specific reason to be. You've already controlled access to the base by only allowing people to enter with proper credentials or background checks. She would not need her ID in most cases unless she left post and needed to come back on.
How did AR access the Arms Room at 8:30pm to get Vanessa’s body? Is a low-level soldier allowed to hold onto the key outside opening hours or is there a place keys are kept and a check out/check in process. Maybe I’m wrong, but I think there must be a check out/check in process. AR went home, then returned later. Did no one wonder why that key hadn’t been checked back in on time?
He was a small arms maintainer. He likely had unaccompanied access to the arms room, which requires a background check and the commander to approve. No key is necessary to open the main door, and if the cage door was shut, he likely had a key assigned to him permanently. The only odd thing that would become apparent at some point is if someone checked the alarm system logs and saw that he came in and disabled the alarm at 2030, but that was unlikely to happen until a physical security inspection.
Why were there no supervisors making sure people were where they were supposed to be? No one ever stopped by and wondered why Vanessa wasn’t at her work station? Did no one try to call her or text her to see where she was? The person who worked with her that day noticed her stuff was there when they locked up. He/she never wondered why she hadn’t been there all day? Again, this is supposed to be a highly secure environment. How could someone go missing like that and go unnoticed?
This was during the self-isolation period of COVID on Ft. Hood. Most soldiers were confined to their barracks during this; there would not be a lot of people out and about doing things. She was out because she needed to complete an inventory.
I'm not sure why you think no one was looking for her - just because they didn't start a massive formal CID investigation in the first few hours she was missing doesn't mean people weren't actually out there trying to figure out where she's at. If an adult you knew didn't show up to an appointment and you can't get in touch with them for a few hours and called the police... What would the police normally do? Do they immediately start an all-hands search for someone missing for a few hours?
Were there no guards patrolling that evening who saw AR pulling a heavy box out of the Arms Room and along the corridor? If it was well after working hours and a lot of things weren’t happening because of Coronavirus, shouldn’t that have seemed suspicious to someone? Do they even have guards?
I'm not sure what impression you have of military bases. There aren't roving guards throughout all buildings all the time. There are MPs that respond to alarm signals and emergency calls and patrol the post in general. That's about it. It's not prison...
I have this image of these supposedly secure areas of Fort Hood as being a kind of free for all with no guards or supervision of any kind. A bunch of twenty-somethings can wander off without their IDs and not come back, and no one bats an eyelid. Heck, they’ll even check them in as present when they have no clue where they are. They can go home with keys to highly secure areas and come back after dark, and no one thinks anything of it. They can pull heavy boxes out of highly secure rooms and through hallways at night and no one wonders what they’re doing. And there isn’t a surveillance camera in sight.
These are gross mischaracterizations. Do you have guards roving throughout the halls of your workplaces at all times? Oppressive presence of force that sees everything all the time? I'm also not sure why you say "no one bats an eyelid". People were looking for her, locally. They were trying to figure out what happened. It's easy to say after the fact, "You should have known she was murdered!" but realistically, how likely is that? After several hours passed (less than 24), and they could not find her, they immediately reported it to CID and an investigation and full search was started. That's incredibly more than you'd normally get in the civilian world.
Vanessa disappeared on April 22nd, yet the witnesses who saw AR pulling the heavy box to his car came forward on May 18. Why did that take so long? Surely, they couldn’t have been unaware of the disappearance for almost a month.
Didn't think it was relevant, or thought it would be silly to report until it bothered them enough to report it "just in case". (MOO)
Edited to ask one more question. If Vanessa and AR were in different units, why was she even over in his arms room in the first place? Do units share weapons? Do they transfer weapons between units? Does anyone who has knowledge of how things are done on bases have an insight into this?
It's possible her arms room did not have a storage rack for the .50cal weapons being referenced, so they were stored in AR's arms room. This is common. It appears he worked in the headquarters company/troop for the battalion/squadron, so this would be a common arrangement. Her being in her headquarters' arms room isn't weird or suspicious on its face.
None of this makes any sense to me at all. It seems like there were a lot of security lapses and a complete lack of oversight from people in supervisory roles. Is this normal on military bases in areas where weapons are stored?
Not trying to be rude, but it doesn't make sense to you because it appears you're unaware of or have little experience with daily life on a military installation. Not much here that you have highlighted is actually strange.
ETA: There is also a weird tone with your post. You act as if soldiers are supposed to be babied or constantly monitored or supervised. They need constant guards, and why aren't supervisors constantly around monitoring them? "Twenty somethings" are just allowed to do whatever they want...
Soldiers have an immense amount of responsibility, and are generally expected to be fairly autonomous. You're cool with handing that same twenty-something a rifle and telling them to go kill bad guys for you (not "you", personally, but "you" in general), but heaven forbid they not have constant supervision in garrison because they're all of a sudden not responsible adults anymore for some reason.