Good question, those kicks has a special underground-rave-rumbling-warehouse-character to them (if we're thinking about the same..). Things i've noticed myself since 1994 but never really thought of...
Read in an interview that he used to spice his kicks with the Alesis Quadraverb at least in the Experience-era, so my personal solution about this issue is: He connected his 909 through the Quadra into an Akai, sampled a kick with the added reverb on a decent level and Lowpassed the whole thing in the Akai sampler. Or maybe he sequenced the kick from the 909 with hi-cutted bassy reverb on it.
Somewhere i think it sounds like a TR-909 kickdrum in original.. But he used his fingertip feelings with the reverb on it, because it can be pretty risky using reverbs on kicks, so you have to adjust the reverb settings so it doesn't cut out too much or just sound like shit in the mix.
Guess the kicks here has high Attack and Tune, maybe not too much Decay - on the 909-buttons, so that they sound pouncy (and not too bouncy) in the original signal. Then the reverb adds the dimension of a longer note and more drawn out in the deeper registers, to make it 'bounce in a new way'.