I definitely like the thought of a hard sci fi game, love the speculative fiction.
I'm no physicist (not yet, anyway) but IIRC NASA's already researching a plasma shield type thing to protect against radiation; the earth's magnetosphere certainly protects us against EMP waves (and other radiation?) so an energy shield blocking energy weapons seems plausible. Lasers could be stopped with dust particles/smoke screens or reflective/absorptive armor, and point defense lasers/railguns/particle beams could intercept missiles to an extent.
That said, there are a few issues... space is friggin cold... stealth would probably be even less possible with manned ships... go with unmanned drones perhaps? Or perhaps not.
Anyway, lots of dronesthe follow up to this would be the requirement for an overseer of some kind. This is where a smaller "fighter" type ship might come in handy...
Anyway, if you go with the "space age stealth beats space age sensors" side of things, "torpedoes" or cloaked (kinetic?) missiles kind of come up again, heck if they're unguided WMDs then potentially they come up exactly as they did in pre-WWII times, with small, nimble vessels zerg-rushing the bigger ships and point-blank firing (relatively speaking) in the hopes of getting a hit. Having cloaked, unmanned torp. boats (probably expendable... maybe, or else they'd just ram the ship with the drone a la the Cole bombing) it would be an interesting mechanic if it could work out in SINS. I always enjoyed torpedo boats vs. dreadnaughts in Fall of the Samurai's naval battles. IMO torps. are fun and frantic to use or avoid.
I'm not entirely clear on things but I think fuel would be the biggest constraint/tactical concern... why not have antimatter represent fuel? whenever you have a change in velocity/direction, you'd need to consume fuel somehow.. not sure how that would work, maybe a toggle ability that disables linear/angular acceleration or consumes antimatter? Of course this might end up taking quite a few ability spots to implement, to say nothing of the probable microing, but if you're going with far fewer but more important/essential ships, then perhaps one or two of the bigger battlecruisers would work like that...
Also, because of the whole no-atmosphere thing, you could use (vac-proof) balloons as rocket-decoys etc.