There has never been a list of how many motherships existed, and I think that there have never been details. I might be wrong, though.
Pre-genocide, the Freespacer population was of 400,000 biological and 1,800,000 automata/SI. Total 2,200,000.
The Yamatai attack has been massive, but not methodical, and most of the Freespacer population resides in starships, especially motherships, which range from "difficult" to "impossible" to track thanks to their low technology, the vastness of space, and the skill in electronic warfare which is one of the Freespacer's strong points, so I think that we're talking of losses of about one third.
That would leave the post-genocide Freespacers with a population of (rounded) 1,500,000, of which 300,000 biological and 1,200,000 automata/SI.
Let's suppose that 10% of the population lived on planets (and is now, mostly, dead). That would leave us with a 90% (now almost 100%) of the population living in space.
Now, I'm going to throw around some numbers. Each fleet is based around a mothership and has a number of support vessels. Let's say that a fleet holds 10,000 'spacers, about 80% on the mothership and 20% on support craft.
That would leave us with about 150 motherships left.
As for their location, I'd guess that they're scattered around. maybe one-fourth in "old Nep" space and another fourth in the area of space the Nep are currently colonizing. The rest scattered around in unknown space and putting as much distance between them and Yamatai borders as possible. Possibly gathering around Null and Void and Journey's End.
Did the Beanfield at Journey's End get bombed? I can't remember. They sure lost the Lighthouse, Halna and Freehold Factory.
Also, about the recollection post: I'd rather make a thread about rebuilding efforts. Creating new ships, integrating them with Nepleslian technology, increasing their numbers (I imagine that, given the destruction of Freehold Factory, the number of biological Freespacers would increase a bit faster than the number of automata, also in an effort to make the numbers more evenly spread).
There has been enough stuff on the Genocide, and I expect Freespacers to look forward rather than backwards now, since their survival and the survival of the ideals of the Free State are on the line.