The hardtop does seem like it would deter people, but in reality thieves will know they can just pull the window. In fact, when my car was broken in to they pulled the window out and didn't even bother cutting the soft top, they just pulled back the driver's window.

I think the sheer size of the hardtop makes it less desirable. 2 seats worth thousands each (from dealer) that fit in the back of a van/suv or a hard top worth less than the value of one seat and requires a flatbed or large pickup truck to transport.