So what does that mean exactly?
That is just how many of each card makes up a Psy Duel deck. Whenever you play Psy Duel in TSoG, the game generates a deck with nine merchants, nine smugglers, and two of each of the rest of those cards, then deals them out to each player.
how much of the game is completed? and how long until you start adding in side quests?
Linear stuff in the main storyline is mostly finished. After the armory raid mission, the game will open up and you'll be able to perform any number of quests to improve your chances of succeeding in a final assault on the city. From that point on, you'll be able to attempt it at any time, but you'll get a bad ending unless you have enough troops to overcome D'Kah and the Ravinale Guard. So in a sense, it'll all be side quests from that point on, in that you'll be able to go through them in any order, picking and choosing as you go.