It is done by enabling or implementing encryption in whatever software is talking between servers.
Companies? Lots do if they care about security. Lavabit for exam- oh wait they died. But other companies still do, Mega for example but probably most cloud storage providers in general as well.
How to determine? Well it's inside their walls, so you can't like... run some command and find out. But they might tell you. Chances are though, if they aren't encrypting between servers, they wouldn't want to tell you that, unless it was part of an announcement that they are changing their ways or something. It's not exactly a selling point to say "heh yes all ur private dataz they are not so privates."