If you need to clear a path through an enemy minefield just to give your fleet a path to attack the planet, sending a massed groups of scouts to detonate the mines is actually the best solution I think. Your fleet is to valuable to leave vulnerable while you are waiting for scouts and fighters to clear them, and if the planet is substantially defended you're going to want your fighters to be attacking the enemies ships, not mines.

Once you've actually taken the planet though, the scout and flak/fighter method works pretty well. Just turn off the auto engage if you are clearing advent homing mines because the scouts don't have the range to destroy them. A single scout and a carrier full of fighters will do the job eventually.

Also, while this is absolutely hated in multi-player, you can use the Z-axis control to just move your fleet over the mines. I occasionally do it in single player if the AI is just being ridiculous, but it is considered an exploit against other human players.

This would generally be true, however in Distant stars mod it's very possible to place the mines where your ships will exit phase space. Esp with the TEC. 

It's a bit hard to fly in and clear mines with scout/fighter/flak combination simply because 50% of them will die the moment they arrive at the enemy gravity well.

Advent mines pose far more of a challenge, since their homing range is just a bit shorter than the range of the decloaking ability on the scout. Yes, its possible to clear them without losses, but its a very time consuming process as you have to manually control which mine to decloak first, otherwise the scout triggers other mines and it gets blown to pieces.