In Watchers of the Throne, a combined force of Custodes and Sisters attack a salvaged cadian pylon. There were 10 Custodes and about 50 Sisters; if I remember correctly. This might indicate some sort of normal ratio of available (non-black ship bound) Sisters to Custodes. So if there are 10,000 Custodes then there would be about 50,000 Sisters.
After all, the actions of Custodes and Sisters have mirrored each other for the past 12,000 years. Reaching a peak at the end of the Crusade, suffering 90%+ casualties in the war in the webway, going into hiding for 10,000 years, and now being redeployed.
Since there are about 1 million Space Marine, yes, I would say Sisters are very rare. But keep in mind that Sisters man the Black Ships and are deployed from them to hunt down Psykers, so there are probably quite a few more on those, and they operate mostly independently of the rest of the Sisterhood.
As far as fighting alongside a guard army for fluffy reasons goes -you sure don't take them to be competitive (
SoS Mini Codex pls,
GW)- It makes perfect sense to have elite reinforcements of any type assisting guard, even one-trick ponies like
SoS. The chance of two showing up is even rarer.