Use marine stainless steel for your fixings. If you are installing in new areas make sure you have easy access to the inside of your deck. You might have to put some access hatches at the inside to facilitate this.
If you put your new hardware where the old was installed you might get away with filling the old drill holes simply with epoxy, otherwise you'll have to do some gelcoat repairs.
This is not as daunting, as it sounds, particularly if you -like myself- have white gelcoat. Here you can buy white premixed gelcoat filler that does not need covering to fully harden. I find it really easy to use (and I've only started doing this kind of work this winter). Filler in other colours is available here but I've got no experience with it.
This is what I use:
Plastic Padding Gelcoat Filler. Other makes are available
You'll need : Gloves, an appropriate facemask, goggles, gelcoat filler, a hobby knife or a drill with a countersink attachment, acetone, white paper towel, masking tape (don't go cheap with that, you'll regret when you'll try to take it off later), a bucket of water with some dishsoap, wet sanding paper of 240, 320, 400, 600, 800 and 1200 grit. If its still cold outside you'll also need a hairdryer.
Wear gloves, goggles and an appropriate facemask/respirator. Make sure you work in a well ventilated area. The chemicals you are going to use are nasty.
1. Scrape the existing hole a bit bigger with a hobby knife or use a countersink drill. Make sure that you've removed any loose/cracked gelcoat and any existing caulk and give the new filler a larger surface to adhere to.
2. Clean with acetone inside and around the hole.
3. Put some masking tape behind the hole and around the hole. The masking tape should be close to the margins of the hole and wide enough around it to avoid putting gelcoat with your putty knife where its not supposed to go.
4. Mix your gelcoat filler as per manufacturer's instructions. Don't prep too much at a time, it will start to harden within 10-20 minutes pending the temperature you're working in.
5. Fill the hole with gelcoat using a flexible putty knife. Make sure that you fill higher than the surrounding surface. You can clean your putty knife once you are done with acetone.
6. The filler needs a temperature of at least 10 degrees centigrades for the filler to harden. If it is still cold, I use a hairdryer over the filled holes for a couple of minutes to kickstart the chemical reaction.
7. Once the gelcoat filler has completely hardened (I wait until the next day), remove the masking tape and start wet sanding. For small holes I never use a sanding block but simply tear off a strip of sandpaper and fold it so it is small (an inch squared) and a bit more rigid. You very quickly get a feeling for how to sand just with a small piece of sandpaper under your index finger. Before you sand, wet the paper in water with a bit of dish soap and wash it out again should it start to clog. Start sanding with 240 grit only over the filled hole til its kind of level with the surface. Continue to wet sand the filled hole and the margin around it stepwise with 320,400,600,800 and 1200 grit.
Then polish and wax.
It really is not difficult at all