Having owned fishing boats and recreational sports boats for years, I find that I prefer a tough non-skid surface on a fishing boat and an easily-replaceable carpet on recreational/sports boat. I am used to always having at least 2 separate boats (fishing vs. recreational sport). But recently decided to downsize to just one multipurpose boat due to lack of time and other commitments. I'm having the same dilemma: carpet or no carpet in my current project Larson 19ft runabout.
Here is my list of pros and cons for each type of a deck surface.
Carpet:
Pros
- feels nice on your feet, all the ladies love it

- Doesn't get hot when the sun is out
- Non-slip
- Cheap and easy enough to replace (if snapped into place)
Cons:
- Gets dirty quick and tracked mud gets embedded deep
- Tough to remove stains
- Holds water longer
- If not dried, starts to rot and smell may even wick moisture to unglassed wood structures (deck, stringers, etc)
- may be tougher to remove (if glued down).
Now on to surface coating like a truck bedliner or specialty paint/coat
Pros:
- tough, durable
- most can be easily washed off
- water dries quick
- water-proofs the deck
- usually non-skid
- looks rugged (which may be a negative thing for some).
Cons:
- too many options for coatings, dont know which ones to trust
- must coatings are black so get really hot in the summer sun
- messy job to apply, may need multiple applications
- if wrong product used, may be pain to remove
- may need to add silica send or some other aggregate to make it non-skid
Hope this helps you decide.