Not that I know of.
I have two drives, A & C, attached via Thunderbolt. Each is divided into two partitions, A1, A2, C1, C2. In Spotlight Preferences I have excluded volumes A1 & C1 (A1 is data I never need to search, C1 is a Time Machine volume). I could try excluding the other volumes, but I don't know how it could help — in Alfred I only have "Preferences" and "Contacts" ticked in the Essentials category, and nothing in the Extras.
The only other "system" link to the external volumes is the iTunes Media Folder which resides on A2, but it is not symlinked, it's just the "iTunes Media folder location" in iTunes. The library itself (.itl etc) is on the internal drive. And anyway this problem happens even when iTunes isn't running.
I've even clicked the "Reset" on the search scope just to make sure, although it didn't modify anything in the list.
Can't think of anything else.