Your guess is as good as mine: one can only speculate as to why others choose to do things the way that they do…
Lead counts in excess of 2 on small fans like this generally correlate with added features usually relating to speed control or speed measurement, 1 wire per feature. The 603-1486-ND includes a speed control and tachometer function, and therefore has two additional lead wires to support those functions. If for some reason a designer chose that specific fan and put a 3-pin connector on it, either the speed control or tachometer function is likely not being used.
The resource here discusses fans of this kind at some length. The Electrical Interfacing, Monitoring, and Control page in particular might be of interest if you have questions about those “extra” wires…