IIRC, agents will open fire immediately on any armed personnel. Which equals heat, eventually, if they get off the island.
Re: Hotel. It's an expensive way to keep 1/3rd of tourists out of the base. The problem is this: wherever your base entrance is, it's probably there to make your life easier and to get your minions and money inside sooner rather than later. Unfortunately, that applies to tourists too. If there is a direct line from the docks to your real base entrance, chances are many tourists will choose the base as the first place to visit when they arrive.
Here's how you do it then. Build LOTS of hotels. Lots and lots and lots. Like 5, at least. Don't pimp them out. Just build them, stick one dance floor or some benches in there, and build another. Scatter them around the island, but make sure to put one at each dock first.
Reason is this. Tourists will only spend a set amount of time in a single hotel. Then they will go out and explore. However if there are multiple hotels, tourists will spend time in more than one (if they walk by it), until they use up their vacation and head home.
So multiple hotels + multiple out buildings + dummy base entrances = almost no one getting into your base except by sheer luck, following your minions or choosing the base entrance as the first thing to explore when arriving at the island.
And do NOT place equipment in them that requires social minions, otherwise you will have tons of social minions roaming the island, getting Maria Mamba'd, or Jet Chan'd, or Katrina Frostnova'd. Build time clocks in them and set them to OFF so no one tries to work there.
I also like to put multiple bee traps in dummy rooms and such. When a swarm breaks loose from the room and starts attacking people outside...I've had huge swarms drive off assault groups before. The unfortunate part is how much micro it takes to keep that stuff working; it gets destroyed on a regular basis and has to be rebuilt. Misdirection traps are solid gold too, as stupid agents tend to give up sooner and/or forget the things they've seen, INCLUDING the traps they just set off.