I have seen a couple boats like mine, that people removed the stainless rails and really updated the look of the boat.

So--

A. Ditch em

B. Keep em

And if I ditch em, what can I put in place of the holes w/o fiberglassing?

pic

Personally I like them.

Very Useful.

They don't look good on all boats, but not bad on your's.

Just my humble opinion.

Another option, powdercoat...

The color of them doesnt bother me, Its the actual rail. Im leaning towards pulling em, but dont know what to put in the holes.

I had high rails on my first cuddy (Rinker), it kind of bothered me. I wondered about cutting the legs down to 2 or 3 inches and then re-attaching the rail? In my case some of the legs were angled so much they would had to have been removed and then re-welded back on. It also looked like I would have to take out the cuddy headliner to remove the rail.
I decided to trade it in

Replace them with a single rail down the middle that is low/close to the deck.