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Thousands of SQLite Databases for each user
See, now that's where it gets sticky.

The question of efficiency is not a problem, it will be very efficient (probably moreso than other DBs) given a few conditions.

If you load-balance, it means either you have multiple processes or multiple machines, so if data is on one machine but not the other (if a file) then it can't really work, so are you duplicating the data?
Would one server process ever need to access more than one of the files?

Maybe it is that you access the data via a common drive/network attached storage? If so, SQLite isn't suitable for that sort of environment (well, not for a flaw of SQLite, but for a flaw in how network file-systems lie about locking - there's tons of literature on this, both on the forum and elsewhere, so I won't rehash it here). See: [sqlite.org/whentouse.html](https://www.sqlite.org/whentouse.html)

You really need to have one server with one direct storage under control of the same OS that is hosting the process that is using SQLite. You may expand to other drives using logic volumes though - same OS, so no problems there.

Some of the above may apply, you have to decide which to know if the solution is perfect or not.