All minions within the base contribute in a very small way to defense at a given time. Only with Guards(Read: minions doing the Guarding task) can you have an active defense. Otherwise its just your minions about their daily lives who might -possibly- stumble upon something happening. Like a man stealing funds, or a homeless guy in the break room eating all the sandwiches.
Lair choice has some impact but again, very small. But for the most part its negligible. For example, A casino has a lot of foot traffic, which may reduce the effectiveness at keeping out X specific person, but they are designed in a cunning way which may prevent actual penetration of the nefarious organization within.
You, are in a small mountain compound. This could be hard to get to simply due to terrain. Nevyn is on a boat, which will make active targeting slightly difficult provided he keeps moving.
As an aside, we should be approaching the time when other base locations may start to become available. These, you will be able to specifically engineer for a positive bonus. An underground base is not going to get much regular foot traffic.
And Hastur, you made this attempt on the first turn. The very first turn, and you didn't mean it as a theft, you meant it as a "I'm taking him OUT." Cmon. Turn one sniping in a game where by default, you're trying to keep everyone from knowing what you're up to from the get go? Please. I'm sayin it here: To find someone, is a successful Plotting roll, and you have to specify yer looking for them. And its gonna be hard usually.
Also.. Why would anyone talk to the guy they just robbed? Cmon, (most)Henchmen aren't stupid.