We had to disable MessageBlobStore::clear() on WMF and replace it with a maintenance script to run upon sync, because on multi-server setups where l10ncache is in CDB, LocalisationCache::recache() is run once per server per language, causing the MBS to be cleared lots of times. This led to DB deadlocks and possibly to other performance issues.
I guess the least we can do is offer a $wg variable to disable clear(). A better solution, suggested by Tim, would be to add CacheDependency::getModifiedTime(), add a way to retrieve the maximum mtime from LocalisationCache, and use that in the startup module to conditionally call MessageBlobStore::clear() before retrieving any module timestamps. This would scale because the startup module is cached for 5 minutes.