I worked for several companies that had their own in-house assembly operations and on average we had 25 boards/array per package. Our average boards size was 12.5" x 6.5" and 12 to 14 layers. The number per packge would go up as the board/array got smaller. I don't remember what the exact numbers where, it was driven by our internal Fabrication Spec that was supplied to the PCB Vendors.
Overall, it really depends on how many boards/arrays you are going to assembly at one run. Less in a package gives you more flexibility to build smaller quantities without risk of contamination to the remaining boards in the lot once the packaging seal is broken. Sure the assembly house could reseal or repackage the remaining boards but it is always better to not risk any contamination that could be caused by the extra handling, especially if the bare boards are going to be sitting in inventory for a while. (+6 months) Handling a large quantity of boards in one package may be a pain but I think it is more of a risk breaking the seal of the large package to only build a handful of boards/arrays.
My two cents,