Regardless if the through hull was factory installed, or aftermarket, it is still just a useless hole in your hull! If you still have the instruments but the transducer is missing, you might be able to get a new transducer, or the correct plug that locks in to the through hull. If you don't have the instruments, but you think you might get some, you may be able to remove the old through hull and put the new one in the same hole, although the odds of the new having the same hole size is pretty slim. If you don't plan on getting instuments anytime soon, just glass up the hole!
Thanks SchockT and Dave! I'm going to do an inventory and start cleaning today as I'm getting ready for the survey and diesel engine check.