From my experience, total size isn't really an issue if the coupling is predominantly local. But you can test that yourself.
But back to via array merging: that is safe in most cases. Exceptions are those cases where the "hollow body" of the merged structure creates a signifant change in current path, compared to all the straight paths through all the individual vias. In those cases, merging the array into multiple smaller blocks, instead of one large block, can be a useful compromise.
Best regards
Volker