It's easy to say that a mobile defense fleet or fighters are the counter. Most people have a mobile defense fleet, but it can't be everywhere at one time. Even having a lot of fighters doesn't make a difference if the siege spam fleet just runs away.
The core problem is the fact that 20-30 siege ships can destroy a planet before your defensive fleet can respond. Once that planet is gone, the siege spam moves to the next planet and the next, completely ignoring the defenses. Once you manage to get your main defensive fleet in place, the siege fleet just runs away to safety after dealing quite a painful blow to your credits.
30 siege frigates take up 360 supply points. That's enough supply for 45 Aerias/Lasuraks/Percherons with Fighter Squadrons, or 180 Arcovas/Seekers, or 120 Jikaras, or 36 Kodiaks/Destras, or 30 Skarovas Enforcers, or...
The Advent could use Seeker Vessels in a 4:1 ratio(which would still be cheaper than the siege force) and riddle the siege ships with laser fire, with the option of using a suicide ram if the planet is going down too quickly.
The Vasari could build 10 Phase Stabilizers for the cost of 30 Siege frigs and use it to transport a part of their fleet to wherever it's needed almost instantly.
The TEC could even build a giant swarm of Arcova Scouts for the price of 30 Krosovs and completely destroy an opponent's trade network, shipbuilding capability and technology level with their bombs, limited only by micromanagement capability. Or put up a defense of 30 Kodiaks for about the same price as the enemy siege force which would obviously be able to kill them faster than they kill the planet. Or better, build 2 Novalith Cannons which make siege frigates obsolete.