Certs are an advantage within a specific loadout, but there is a "soft cap" to what you can spend on a specific loadout. If that "soft cap" can be reached fairly quickly there won't be too much of a difference between relatively new players and someone who's been playing for years. Obviously, there will be a few things beyond the "soft cap" until they get to the actual hard cap (100% certification for the loadout), but not necessarily providing enough of an advantage in and of themselves to make enough difference to matter. Beyond that "soft cap" is going into other loadouts (having options gives indirect power but not in a way that unbalances the game as long as those options are equal) or going for that "hard cap" to have a very slight advantage over the general players (but certainly not one limited to pay-players).
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ATM it's really really really slow, to the point where you can't keep up with someone getting 30 certs a night for paying a sub, seeing as certs are upgrades.
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SOE won't have passive gain's be greater than active gains, and likely won't have them stack. Not only are they interested in balancing the game, but they are interested in selling boosts on top of Subs.
Even if initially a new player can't keep up with a subbed player, the subbed/boosted player will still reach the soft or hard cap allowing the un-subbed to catch up at least within that loadout.
Related note:
I wouldn't be surprised if this was eventually topical to the issue of XP/Certs (Certainly it already is with Boosts):
http://penny-arcade.com/patv/episode/energy-systems