Here is an idea that , i think, might help solving both issues at the same time.
- Remove Supply Convoy from the list of detectable missions in the same way we can't detect UFO reinforcements directly
- Change Supply Convoy to a quick response missions, possibly with a few more days than retaliations OR force 100% infiltration like HQ but possibly with a faster infiltration than regular missions (as you must prepare an ambush but not really infiltrate troops in the middle of nowhere)
- During Guerilla missions, one Officer (or maybe just any pod leader) have a chance to drop some "ADVENT orders" among other loot. Once recovered or possibly researched (a quick research) those orders reveal the location of a moving Supply Convoy.
- Players will want to fight in Guerilla missions to get those orders and be able to run the very useful Supply Convoy missions. As a result Stealthing a mission will be viewed as an option for a mission with a short timer or one you really want to complete (like a liberation chain) but not the best way to complete every mission.
- No need to nerf stealth (or at least not as hard)
- No way to abuse 0% supply raids and break the economy of the strategic layer
- Balancing raids is easier because you know how many enemies the players will face