I haven't tried large assemblies yet.
I have a project that worked its way up to about 100 parts, mostly composed of several copies of a dozen parts. Placing and constraining all of the parts in Onshape takes time, and not all of it is as efficient as it could be. In software like Solidworks or Inventor, there is a way to make inserting 10 copies take only slightly longer than placing 1 part, however, Onshape does not yet have that functionality (AFAIK) and placing 10 copies of the same part takes 10x as long as placing 1.
If at all possible, break down your assemblies into sub-assemblies. It saves lots of time in Inventor and SW and it will pay off even more in Onshape if you do. Set up mating icons in each sub-assembly, too.
I have yet to investigate whether Onshape can communicate part names to a BOM and/or have expandable sub-assemblies in one BOM. Since neither Inventor or SW do this perfectly themselves, this is an area that Onshape would score a crippling blow to my preference for its competitors.
No one believes the theory except the one who developed it. Everyone believes the experiment except the one who ran it.
STF
