Quoting from @Chahk's answer to another question:
Longer boot-up and shut-down times when the system mounts/un-mounts all of the apps stored on SD Card.
Apps that were moved to SD Card are not stored in plain sight to prevent rampant piracy. Instead, Android sets aside some space and creates a virtual partition for each app that you move. This means that at the initial boot-up, all these virtual partitions need to be mounted before apps stored on them can be accessed. The same holds true when you turn the handset off - each virtual partition is un-mounted before other shutdown processes can happen. Depending on the number of installed apps this can take an extra minute or even longer for the system to "stabilize" upon boot-up (and about 20 extra seconds for shutting down.) Once this happens though, launching these apps doesn't take any longer than those on internal memory.