I reported problems with the eAlert indexes a few years ago (May 2011):
http://metastorm.processmapping.com.au/post/eevent-and-ealert-primary-keys-should-not-be-clustered-5258075
Basically the eAlert primary key should not be clustered, as it fragments the table very quickly, and the eAlertType should be referenced.
It appears that the situation is still the same in 9.3. On top of the table becoming very fragmented when used a lot (and it is the most commonly inserted to and deleted from table in the system), but if you do not store deletion alerts, the index will hardly be used (and may not be at all) if you have lots of Watch alerts, which is very common.
It seems simple to fix, and performance improvements would be significant in even modestly sized systems.