The only reason to cut the top is to unlock the doors. Realistically they are not going to be entering through the top or working from the top of the car to remove a radio. Breaking a window would be an easier way to gain entry. The cut needs to be big enough to stick something inside the car to reach the unlock button (on center console) or to reach in to access the unlock button.
I am curious about how common it is for them to be broken into as I'm not sure there is a lot in there that thieves target. I own an s2000 so this is of particular concern to me. It is very common for s2000 owners to have their tops cut for thieves to gain access. This is because the demand for s2000 seats, steering wheels, and instrument clusters is pretty high. The civic ricers want them. It is not unheard of for an s2000 to be "totaled" by an insurance company after just those items are stolen.
I suspect without such demand for e46 parts having your top cut may be less concern on the convertible models?