To hide it from Barney and Otis. Duh.
You are supposed to find out that Xen has been researched before in Questionable Ethics. Any evidence before that point would ruin that shocking moment 
The facility is not secret. It’s kinda hard to call something secret when you have boxcars, crates, shipping containers, trucks, etc with the Black Mesa logo clearly stamped on them. Not to mention the trains are likely loaded up in the city, then sent to Black Mesa, allowing anyone along the railway to see the logo’s on all the cars.
True. But, you could have inconclusive and obscure hints toward something that only us who know what is really going on could identify. Partial skeletal x-rays, substance sample references, blurred xen images being analyzes with cryptic references.
But the stuff they do is secret :retard:
Which goes back to my other point, you don’t just leave top secret things laying around for everyone to see, especially if some of the employees aren’t high enough level to know about it (Gordon). 
Exactly. It’s not like the doorman at Langley has access to every CIA intelligence report.
Yeah this. That was the whole point of the chapter, plotwise
Gordon is in Sector C, in the Anomalous Materials Laboratories, the aliens are contained in Sector E, in the Advanced Biological Research Lab.
Don’t you see headcrabs in tubes shortly after the resonance cascade? I think that would imply research is being done.
they teleport into the tubes, but I don’t think the science team intended them to, given the nature of the experiment.
Yes, they wouldnt have aliens like headcrabs there BEFORE the portal opens.
yes they would, look at places like the labs in Questionable Ethics and the tank in Apprehension, they obviously have had Xen aliens on Earth for a while.
Well yeah, because the entire point of Questionable Ethics is to find out they were studying aliens. Hence the name ‘questionable ethics’.
Exactly my point…
But you see them studying the aliens before that…
No you don’t. Not in Anomalous materials, anyways.
What about the scientist who says “If the world finds out what we’re doing down here…”
That pretty much confirms the secrecy of the Xen shit.
Not exactly. What if he was refering to the less-classified AM experiements screwing with the fabric of the space-time continuim? Or something else that would prove to be contreversial?
Really, half the things in the BM facility apply to that sentence. Hell, maybe he’s talking about the lax safety regulations.
“If the world found out that not all employees wash their hands after using the restroom…”