Because some analogue, not pwm fans might get extra noise under pwm regulation. IIRC In normal 4pin pwm fan there is separate wire for pwm synchronisation, that solves that issue, but with analogue fan with normal 3pin these voltage spikes might differ at different rpm at which point coils should actually charge and push to turn rotor and at one position have more voltage, at different less, so possibly resulting in that extra noise.
Otherwise pwm of course is better then analogue regulation in several ways - it's circuitry is cheaper, as doesn't require monstrous heatsinks to dissipate redundant power, it can handle much higher current, with pwm minimum rpm-s can be lower (as less of a problem minimum startup voltage to start turn motor, because it's always full 12V or 0V). But probably because that pwm rpm regulation is newer, and many analogue fans/pumps exist, some choose analogue regulation as safe bet for everything. (eg. Aquaero).



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