I have two Tacomas, and have soft tops on both of them. One is a Bestop. the other is a Softtopper, I like them both. Obviously there is the lack of security that is available with a hard shell, but as stated drawers and lock boxes will help.
I am also looking for a rack to go around the soft tops. There are a few out there. Softopper has a couple of racks on there site.