If you do it right they won't even get a shot off but you have to let the crew do the shooting while you con the boat, it's kinda fun to chase them down.
I assume you want to shoot them yourself. It's fun that way as well.
The best way to mod the game is to just give them a try, with JSGME it's easy to add any of the super mods, if you don't like it you can easily take it out.
Start with just TMO, RFB or FOTRS and see what happens. You can always go back to stock but I don't think you will.
If you like stock try Webster's Game Fix Only mod, Fixes a lot of things without changing game play.
Plenty of help here if you have problems.
Magic