Hole Saw
A drill-powered hole saw is, by far, the best way to go and a tip is you want to buy them at Home Depot or some place like that NOT at boat stores. I prefer DeWalt hole saws -- maybe because they are yellow, I don't know, but I have DeWalt cordless drills and they, in my opinion, are pretty much the best -- and you can get them in a variety of sizes at nearly half the cost of boat supply stores. Be sure to get the DeWalt mandrels, too. These are good saws that cut clean, quick holes and last a long, long time with just reasonable care.A good idea, too, is to stop once in awhile to clean out the "groove" the saw is cutting as it makes the cutting go quicker. You can also use WD40 to both lube the saw during the cut and to also keep it a little cooler so you don't melt the plexiglas or Lexan in your hatch. My guess is that unless someone replace the acrylic in your hatch, it's typically not Lexan since Lexan is much more expensive that sheet acrylic and boat manufacturers are not known for installing this kind of cost-based luxury in your hatch. It might be Lexan, but I'm a little doubtful based on experience. One thought might be to replace the acrylic if it's getting old. I did that in mine, but I replaced it with 1/4" tinted tempered safety glass plate and it's a lot tougher than you think. I've bounced winch handles off them a few times with no damage at all, but that's not really a practice I'd recommend! You can have the glass company cut the appropriate size hole in the plate and you can install the deck ring in the glass using 3M 5200. Believe me, it won't leak!! And, you can install the interior finish trim ring on the inside the same way for double leakproofing.I'm absolutely NO wizard with a jig saw so I can't really recommend that practice for this kind of work. When I use jigsaws I use them carefully and, as the other gentlemen well-suggested, use a sanding drum to clean up the cuts. I'd stick with the hole saws.By the way, pricewise, you are looking at about $30-$40 for the hole saw and mandrel and my only other piece of advice is don't use a cheap one.Good luck.