Yeah, there are ways around drilling holes in the boat, but you'll need to be creative. Here are 2 methods:
I rent my yaks from the Marine Corps, so I can't really drill holes into them, but I get them almost every weekend, so I do need pole holders.
1. So I've devised a PVC pipe pole holding system that I insert into the scupper holes in the kayak. Those are the holes that go through the yak to allow the water to drain out and keep the yak balanced. The thing looks like an "H" with small pipes to fit down into the drain holes, and then it forks up like deer antlers at the top with 4-2 inch wide tubes going up about 11 inches for my poles, net, gaff and the like. I just got crafty with the fittings for different PVC pipes at the hardware store to put the thing together. Here is a pic:
La Jolla Kelpin'.jpg
2. Another option is to use a milk crate. You can cut 2 inch diameter PVC pipes to about 11 inches long, and use hose clamps to attach them vertically to the inside corners of the milk crate. Then lash the crate behind you to the deck of the yak, and use the pipes as pole holders. The crate also comes in handy for storing xtra stuff. This method gets a little top heavy, which will affect your balance going into and out of the surf, like we do here in California. But in rivers and bays and such it's manageable, provided you secure it well enough. Like this:
cowboy clay fishin LJ.jpg
Hope this helps.
Willy