Gav Thorpe’s Corax anthology provides an explanation for this in the Weregeld story on p. 461:
It used to be that the Shadowmasters had hunted in squads, using their unique Corax-gifted abilities to sow discord and terror amongst their foes. Now they worked alone, their number reduced to a handful amongst all the legionaires of the Raven Guard.
That particular story takes place during the Horus Heresey, not too long before Horus makes his advance on Terra. So, after the decimation of the XIX Legion on Istvaan V their numbers would have been somewhat depleted – the number of surviving Raven Guard was something like 3,000 from memory – and it would seem that attrition had reduced the Mor Deythan numbers further throughout the remainder of the Heresy.
That does not answer the question as to why more were not found amongst the future geneseed-enhanced warriors of the Raven Guard, though…