I've been through this , owned a few tinnies, the last one was a quintrex 600 Navigator with a full floor and CC. With any tinny, you really need to lift the floor once a year to clean it properly. As for the actual deck finish , I've tried plain non-skid paint as well as carpet glued down. Non-skid paint is certainly easier to wash down. Anyone who makes a practice of just landing thrashing pelagics straight onto carpet is looking for a stinking trashed deck in no time. I always had a kill bin--just buy a good lug bin from a commercial fishermans supplier, stick them in head first, then bleed. But it isn't always possible to do it cleanly. As well as mashed bait. Washing/scrubbing helps, but I found the best way to really keep it from stinking was to use a wet vac and detergent. Just wet it down well, spread the detergent around, then wet vac it up. The colour of the water you will get out is...interesting.
No one wants to get on the boat that stinks before you even get it wet. it's not hard to keep it sanitary. I think that glued down carpet is actually easier to keep clean than loose carpet, I've never had any success at keeping that stuff pleasant.
anyway, I won't be posting much for a while now, going away for a month's fishing and camping where internet availability is patchy.