Tortoise burrows typically have half-moon-shaped entrances that approximate the shape of the shell. The angle of the entrance (about 30 degrees below horizontal) also can be a helpful criterion. However, as you say, some can be hard or impossible to identify.
Active burrows are free of debris, vegetation, and spider webs at the mouth; usually have tortoise tracks leading into and away from them; and often have tortoises in them. Tortoise researchers and surveyors insert video cameras on long probes into burrows to see the interiors and determine whether or not they are occupied by tortoises. A permit is necessary to do this.
Gopher tortoises and armadillos can coexist, but armadillos often eat tortoise eggs and occupy tortoise burrows. As you probably know, armadillos are not native to Florida.