I wouldn’t advise you to use BuddyPress if you don’t have a specific use for any of the special features that are offered by BuddyPress.
From what I’ve seen from the BuddyPress core is, that it doesn’t change any core existing WP functions. So I don’t believe that BuddyPress actually changes the handling of user_meta. I seriously doubt that BuddyPress changes anything (wether to the good or to the bad) in regards to the performance of the user handling in WordPress.
Also from my experience (had up to 15.000 users in one install until now), the performance is still good with vanilla WordPress. No performance degradation measurable. Especially if you have object/database-caching in memory.
If you reach the performance limits of the core API functions you could still easily change your application to hand-crafted and tuned SQL queries and optimize your query and index structure to deliver maximum performance for your specific user_meta queries.