The physical set has all the counters from the boxed set plus new ones from SFoS (although it is apparently missing the Lakara).
There is a mistake with the pdf version of the SFoS counters, it is missing Sentris, Starfuries, Thunderbolts and the Lakara. However, Sean-Kahn has done fighter counters, see here: http://www.mongoosepublishing.com/phpBB2/viewtopic.php?t=31565&highlight=counters
These official sets don't include any ships released after SFoS - Drakh, Dilgar, ships from Armageddon and ships new to 2e.
There are a number of fan-made counters, take a look at the player resource thread.
New official counters are planned.