In order to give a user reputation for a suggested edit being approved, a "vote" has to be created. The VoteTypeId is 16 and labeled "ApproveEditSuggestion" - and it gets created with a reputation increase of 2 and assigned to the last user who voted to approved the suggested edit. In cases where the OP approves the edit, that will always be the OP - otherwise it's just the third user to approve it, and sometimes the Community user in the event the edit was improved.
Now for normal users, you won't ever see this causing a big problem. You need at least 2,000 reputation in order to review suggested edits, which also means you can't easily delete your account (you have to talk to us, and we have to manually review your account before it actually gets deleted by the system). Ergo, we can prevent mass damage from occurring by transferring your votes to the Community user before your deletion goes through (if need be), which would preserve all of these +2 votes anyways.
Then we get to the lower-reputation users who approve edits to their own posts. They don't have to talk to us before deleting their profile - they just have to wait for some automated emails to fire off and they can complete the entire process without saying a word to us.
Since there is no oversight into these users and deleting their profiles, it opens up a possible abuse scenario where users could create another profile, post a single question or answer, and then suggest as many edits as they want having them all instantly approved by the post's owner. They could then delete the other profile and leave no trace of voting irregularities in the system since one of the users is now gone. If no one notices this random post with an edit history filled with nonsense, then they just gained a bunch of reputation that we'd never know about and they definitely shouldn't have.
Problem solved: we already delete all of their votes when they delete their profile. So all of those suggested edit approvals that went from one user to the other get deleted/reversed, and the reputation disappears.
Essentially, deleting these suggested edit approval votes is no different than deleting the users upvotes, and no more or less fair to the user affected with the reputation change. It's just a part of the user deletion process.