NPN Transistor Data Sheet, Source vs. Sink Current
For NPN (and N-channel MOS) they defined Ic (or Id) to be current going into the collector (or drain) and Ib going into the base. It is that simple.
Often PNP (and P-channel MOSFET) datasheets DO use negative signs for the currents and voltages, remaining consistent with the sign convention for NPN (and N-channel).

Image from 2N3906 datasheet.
The only point of inconsistency is that some companies report currents for both polarities of transistor as positive, thus using opposite sign conventions for NPN and PNP. While I can't say WHY they do this, I will say that it shouldn't confuse anyone who has at least a tiny bit of experience.