One: No reason to take the guts out if you don't care about weight or doing heavy customization work on the inside. If you're just putting in flexwatt and a light, you shouldn't need to do anything near the freon tubes, so taking them off is unnecessary.
Second: Yes, a hole will let cold air in. Run your cords through and then patch it up as best you can. Your flexwatt should be able to handle the extra little bit of effort it takes to maintain temps with a little hole.
Lastly: No, don't do a hole for each item. Make one hole and run each cord through that hole. No reason you couldn't do three holes, but why would you? Best to only have to patch one, plus that keeps all the cords in one place.
Best of luck with your project, make sure to post up with the final product!