I'd be surprised if there wasn't.
"Are there court cases in which the feds have relied upon substantial indirect effects and aggregation to assert commerce power over aviation?"
Only if it was challenged.
Look. My point is that your private, non-commercial intrastate flying is only regulated when you're having a substantial effect on the interstate commerce that Congress is constitutionally regulating. The same is true for guns and drugs.
Excuse me for being blunt, but it appears to me as though your objection is personal, not constitutional -- you don't think Congress should be regulating guns and drugs.