I don't think I'd put more than maybe 15k files in a single directory. Some QShell utilities run into trouble at around 16k files. But I'm not sure I'd store them in a directory in any case, except maybe for ones over 16MB if that's a significant fraction of the total. I'd possibly look to store them in CLOBs/BLOBs in the database first.
Storing as individual streamfile objects brings ownership/authority problems that need to be addressed. Some profile is getting entries into its owned-objects table, and I'd expect that profile to be getting pretty large. Perhaps getting to one or more limits.
By storing in the database, you drop to a single owned object.
Or perhaps a few similar objects... There might be a purging/archiving process that moves rows off to a secondary or tertiary table. Hard to guess how that might need to be structured, if at all.
Saves could also benefit, especially SAVSECDTA and SAV saves. Security data is greatly reduced. And saving a 4GB table is faster than saving a thousand 4MB objects (or whatever the breakdown might be).
Other than determining how the original setup and implementation would go in your environment, the big tricky part could involve volatility. If these are stable objects with relatively few changes and few deletions, it should be okay. But if BLOBs are often modified, it can bring trouble when the table takes at a significant fraction of DASD capacity. It gets particularly rough when it exceeds the size of DASD free space and a re-org is needed. With low volatility, that's much less of a concern.