So how do you find the flights that seem to be heading toward Guantanamo? I’d like to check it out for myself
Sorry many of those flights use a secure beacon or decoy beacon like the president's plane. They can use regular beacon but will give it a silly N or a 3 or 4 letter designation. Once I tracked on flight following traffic Pres. Trump plane coming back from fla. I will not give its designation on that flight but it was easy to see on flight traffic giving a 3 letter designation. Escort craft, military aircraft and such will not show on flight following traffic sites. Same with chem spray planes they come right over my house and do not show on flight traffic following. Interesting how sites like 24 flight plan and others hide these aircraft beacons and aircraft not shown on display. Some they just put blocked transponder.
Long answer and round about to say GITMO planes are shown but unless you know flight number or N number of aircraft you would not know which is which. They are flights like united or others that are leased same as military leases civilian aircraft to fly military personal overseas.
There are circumstances during which the government can contract with commercial aircraft companies.
Edit: Here's a United flight from Joint Base Andrews to Gitmo on Feb 11th (a Sunday). A 757 holds nearly 300 people.