OK, skipping right past the controversies and having never played a game of Malifaux, card counting relies on a huge number of trials and small percentage benefits over a long period of time in Vegas. The best card counters in the world MIGHT get 5% ahead of the house across every game they play. The big deal is that when they're at a big advantage that $5 bet suddenly becomes a $10,000 bet. In other words, Vegas card counting means very little 99% of the time but capitalizes hugely on that other 1%. In Malifaux, you may well find its not worth the effort required for the benefit of knowing that three actions every five or six games will be shoe-ins.
Here's some basic thoughts and some basic math on how to deal with it:
Your deck has 54 cards.
Not counting jokers, the average card value is 7.
13/54 (24.01%) of the cards are of any given suit.
So two VERY dirt simple, very rough things you can track are high/low and whether a given suit has shown up more or less than it is likely to. You can also keep track of jokers, of course but that's hardly counting.
Every time you see a card worth 8 or more modify your count by -1. Every time you see a card of 6 or less, modify by +1. You count can (in theory) be anywhere between -24 and 24 but is likely to hover around 0.
At +/-4 the odds move from 50% to 54.5%. to At +/-8 the odds have moved from 50/50 to 62.5%. At +/-12, the odds are 66%. Unless you're very deep into a heavily stacked deck, this is not likely to matter much. Shy of +7 or so its less than a 10% bonus. This could probably be tuned based on an important target number but the odds would have to be recalculated. If you're really on the ball you could also track your opponent's cards.
Suits might be easier to track. Keep track of the number of cards you've seen (your hand plus discard) and the number of a given suit you've seen. The math is somewhat tricky and I'm sure there's a shortcut but its late so here's what I've got.
Subtract number of a given suit seen from 13
subtract number of total cards seen from 54
This gives you a ratio that you can turn into a rough percentage and that's your odds of getting that suit on your next flip.
One thing: don't forget your hand!