It seems like Naval Bases and Depots lie on a continuum, much like Starport Classes. Consider the capabilities of Naval Bases and Depots:
"N" is typical of naval bases; however, there are perhaps more capable naval bases. "N2" bases conduct research; the only example I know of for this base was HRD back when it was first built. The "N3" bases include a mothball facility; the example of this one is Trin. In both these cases, the naval base could be considered more than just a typical naval base: they are partway to being proto-depots.
Code:
Depot N N2 N3
Supply/Mtc/Refit x x x x
Prototyping x x
Mothball Facility x x
Construction x
Training Fleet x
Security Fleet x