The Ion Beam's chance to arc through shields is based on the
hard flux level (with 0% chance up to 10% hard flux, going up to 90% chance at 100%), and it's very expensive both in terms of OP and flux. "Unfair to play against" is definitely a concern, but hopefully that'll be enough to balance it out; it's really not meant to be something you can easily jam onto direct-combat ship. That, and there's some counter-play available in terms of managing your hard flux. Could tweak the probabilities at some point, too.
The Pulser looks pretty good. I'm a bit worried it'll directly compete (and lose) to the heavy blaster for a place in the medium mount. The limited ammo clip, shorter range and (i assume) lower damage per shot doesn't seems like a good trade-off for the bonus EMP effect and burst dps.
Your guesses re: stats are correct. In addition, it's a bit less OP, a bit more flux-efficient, has a significantly lower sustained flux cost, and can really lock down a target if a full burst gets through shields. I think that should be enough to carve out a niche, but yeah, again it's something to watch out for.