Yes, normally gutting or modding an air box will result in leaning out your sled a bit.
By your saying that the carbs have bigger jets "I remember from previous cleanings", I assume you've had this sled a while? How does the jetting look on the plugs when you check? I wouldn't worry about noticing that the air box has been modded and then start worrying that you need richer jetting if you've had the sled a while already and it hasn't burned down. I would also assume that if you've had it a while you have certainly checked how the jetting looks. I'm not trying to be rude, but it is a super important thing to check jetting when acquiring a used sled with carbs. Many people have bought a used sled from someone and then burnt it down. Buying my sled would be a perfect example. I average riding at 5000' and up and have my sled jetted accordingly. If someone bought it and then did all of their riding at 1000', well they're going to burn it down if they don't richen it up. If you know that the carbs have bigger mains, then one would assume that the previous owner richened it up when he modded the air box...but other factors come into play too, like elevation and temperature. And we all know how the word assume breaks down.
My opinion is to do some low range, mid range, and full throttle runs if you haven't already, read the plugs, and jet/adjust it accordingly. If you ride a fairly wide range of elevations, be sure to do these checks at the lowest elevation area you ride.
Remember, fuel always stays the same unless you change jetting, but air is more dense the lower you go in elevation. So, if you jet it at 5000' and it is spot on perfect, but then go ride at 2000', then there is more air and you will be leaner. Warmer temps are richer and colder temps are leaner as well, but this is less touchy as elevation unless pretty drastic.