A few days ago gridlore
had a post about "Who built the Batcave?" I'm repeating my reply and expanding on it.
Do what rich white people do all the time. Bring in "illegals".
More specifically, hire folks with the right skills from all over the world. Bring them in illegally (which also lets you keep them from knowing where you are taking them).
Use refitted cargo containers. Which can also be used for housing on-site. Wayne enterprises could probably use portable housing of that sort in a lot of places anyway.
So all the workers and contractors know is that they got hauled somewhere, built some neat stuff, never saw anything outside the cave, and got paid very well for it.
You could even split things up so that no one group built more than a portion of the stuff. So even if they talk, they can't give away anything significant.
Heck, set it up as a special business unit in Wayne Enterprises, and keep doing the same thing for other heroes, the military, and intelligence agencies.
Inn a world with supers there are likely *several* such outfits.
And in some universes, they may get treated like the Whateley campus. They are hands off because *everybody* uses them, and *nobody* wants to have them (or their personnel "leaned on" to leak info about jobs they've done.
Picture having the Justice League, Lex Luthor and bunch of other "heavy hitters from *both* sides of the law "somewhat upset" with you? Or in the Marvel-verse, the avengers and Doctor Doom.
Though the business has other perils.
"What were you thinking of? Using a Lexcorp QX-3000 in a hero's base?"
"But it's cheaper and more reliable!"
"If a hero *asks* for stuff from Lexcorp, that's fine. And if they aren't one of the ones who has an ongoing feud with Luthor, you might *suggest* it as a possibility. But never do something like that without checking."
"And while we're on the subject, be really careful about using Wayne Enterprises gear in projects that might not be entirely legal. They've blacklisted folks for that before. We don't want to be the next company that they won't sell to!"