All of your phrases are reasonable. I personally would avoid the math, and say "I ordered seven donuts, but I only see five." This is clear, it communicates accurately, and it limits itself to facts. "I only see" avoids placing blame or saying whose mistake it is. It also better matches what is on the sales slip. The sales slip will either say "7" or "5." There isn't going to be any number "2" on the sales slip. "Two doughnuts are missing" vaguely suggests that someone actually counted out seven, and then two were taken away. They rolled under the counter, or were absent-mindedly given to somebody else. "I only see five" states the facts with out suggesting anything at all about what happened to the two doughnuts. But all this is overanalyzing. In real life, all of your phrases are clear, and all are polite enough. Telling someone that you think they made a mistake is always going to be unpleasant no matter what words you use. P.S. "Donuts" is a correct spelling, but I am an old guy and I personally prefer the spelling "doughnuts."

Hi Gabriel, In these situations, be as objective and kind as possible. I would say, "Hi, I ordered seven donuts and it seems that we're still missing two. Can you help me?" If you want to say "There are two donuts missing" that works too, just remember to say it nicely :) Hope that helped!

Another option is to politely say, "Excused me. I think you have short-changed me. I ordered 7 donuts". The term "short-changed" is commonly used when you receive insufficient change with your cash payment However, it can also be used when you are given fewer items than you ordered or paid for. Hope this helps

All three are correct. The choice "There are two donuts missing." is very, very natural. In my opinion, native speakers use the phrases "There is ..." and "There are ..." frequently and non-native speakers use it rarely.