Anecdotally: A general rule of thumb that I have experienced in my ventures is if the GDB is serving as the back-end for a web application, many more times than not (~85%) it is stored in a RDBMS.
The advantages of doing so far outweigh the disadvantages in most cases:
1: Easy backups and logging of activity
2: More control over user permissions
3: Centralized integration with other, nonspatial data (the web developer doesn't have to go through extra hurdles to access the spatial data)
- Extra fees in licensing (If you are already paying for ESRI licenses, this is probably a minimal cost anyway)
- Extra resources required for DB setup (again rather minimal, because for most spatially enabled databases going from FGDB to RDBMS is not a monumental task)