Just do it, you will get good results with either. Caulking has more to do with prep and technique than it does with the compound used.
For instance, the PO of my last boat smeared silicone all over everything, looked like ****, and did not help deck leaks at all.
The hardware bedded on my 1968 islander was done correctly, and it still doesn't leak. This was with 1968 caulk technology, so you probably don't have a thing to worry about!
Not so, I'm afraid. There are three major types of sealant: silicone, polyurethane, and polysulphides.
Polysulphides are great for general sealant projects.
Polyurethane is PRIMARILY an adhesive. 3M 4200 and 5200 are the standards. Great for their intended purpose, but unless you are looking for an ADHESIVE, do not use it.
Silicone is garbage. It is unreliable and, more importantly, leaves behind a chemical residue. This is a major issue if you ever need to paint the boat. Silicone has no place on a boat. Ever. There's always a better choice.
A couple others:
BoatLife LifeSeal - a silicone/polysulphide hybrid. It's great stuff and appropriate for plastics. Pure polsulphide can eat plastic.
Butyl Caulk or Tape - also good stuff. It remains pliable for a very, very long time and is great for portlights. I've used frequently for this, though when I recently replaced my plexi ports, I went with LifeSeal and was very pleased. One negative about Butyl Caulk is that it is messy.