I think that qualification in the manual has since been revoked. I have had zero problems with the batteries.
You're right there's a flyer dated from March 2003 with the Sea&Sea YS-90DX stating that NiMH batteries can be used for the YS-series strobes (20A,25DX,40A,60TTL/S,N,90TTL Duo,90DX and 120TTL Duo). Sea&Sea mentions that the battery life for the YS-90DX is 260 flashes with a recycle time of 3 seconds based on full light level. They also mention that these specifications depends on the battery specifications, recharging status and frequency of use.
What this flyer does not say is that if you're expecting the YS strobe to mimic the pre-flash and flash of the internal flash of a digital camera, you may only get the pre-flash.
Clément