Scouts are a great counter
if there were a cap to them, yes perhaps.
please take a look at this savegame.
jump_before_dump.zip
i'm about to jump to a wormhole where the AI has placed no less than 2500 mines.
my fleet (including 6x level 5+ capital ships) will get vaporizes within 20 seconds.
sometimes this also gives me a minidump after a few secs because my 3.6 GHz E8400 can't handle it 
I played this game for many more hours now and pretty much every enemy world or chokepoint looks like this.
it takes an insane amount of navigators and micro-manage-clicking hundreds of mines to get through this.
and the only way to do this without losing too many ships is a fleet of carriers/transporters on the edge of the gravity well.
eventually I cleared an asteroid "mine"-field with about 500 mines on it using 40 vasari transporters and a couple of scouts.
it only took me about 15 minutes micromanaging this when the AI dropped in and deployed another 800 mines in 5 minutes just by flying by (he didn't even attack).
please - maximum mine cap 100 per gravity well and increase build-time a lot! 
otherwise it's currently unplayable in end-game 