As to you first question, it could fill up. There will probably be CL of some kind availabel some place- esp if you are flexible among the three Disney deluxes in that area: BC/YC/Bwk. If you want a certain room category though, you may want to book as soon as you are able. I can tell you many times when we've stayed CL it was full for the night.
Generally speaking, WDW is great with allergies. You'll probably do better at TS places, where the chef will come to your table. If your son's allergies are along the lines of easy to avoid foods- like strawberries- simply staying away from them may be easy enough. If they are more along the lines of your wheat allergy- i.e. an ingerdient that is common in many foods- then most certainly let the CL staff know. Usually they will have it noted on all your ADR's. (so long as they know about all yoru ADR's) If you arrive at any ADR, and STAFF doesn't mention the food allergies, tell them.
As for CL food itself, experiences do vary slightly. If again, you know certain foods are okay for you, that's often the quickest route. Staff may also offer you prepacked allergy free items- esp for things like brownies, cookies. Then again, it's possible you will be slightly left to fend for yourself. My CL allergy exp, was at GF, which went above and beyond. There the chef came to talk to the person with the allergy, and went so far as to prep specific foods, at a secific time. That may only be true at GF though. It took time to talk to the chef, and we were held to getting the breakfast food delivered rather early- i.e. when the food was prepped at 6:45am.
Also, being a DIS vet, having read a tragic post about food allegies- I'm also going to avise you to always carry your emergency meds at WDW. It might also be smart to bring along a box of something like safe granola bars to have on hand.
Last, DO look on the DISabilities section of the DIS- lots of good info there.
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Since I love the "planning" part of any trip, I'd hate to turn over this duty to a stranger.
