IMO, the implications of Ion Weapons are pretty sticky, but I think there's a few questions you have to ask yourself anytime you introduce "imports" from some other universe. I assume you're talking about the Ion Weapons from Star Wars.
* The biggest question I always had watching Star Wars was - "Ion Cannon are so effective. Why would you ever use anything else?" (also: Big Ion Cannon seem pretty common the SW universe, why would the Empire be caught so off-guard by them?). This is a question you'd have to ask introducing them. If they're really effective - nobody would use anything else. Like in SW games, Y-Wings carry ion cannon ... but they seem pretty good. Why don't X-Wings carry them? In a "real" universe where people choose things for effectiveness and cost, there's a certain blandness as everyone moves towards the best solution, unlike video games were players want variety so people carry around shotguns, assault rifles, and a submachinegun because bulk and weight doesn't mean anything and each weapon is unrealistically coded to have a niche only they can serve.
* Weird weapons are always prone to abuse by people who are always looking for advantage, like the players. Be it grappling rules in D&D, tranquilizer rounds in more RPGs than I care to talk about, and Ion Weapon in SW. There's also the implication that if the players have thought of these abuses, there's trillions of people in Charted Space - millions of people over the course of however long Ion Weapons have existed in the 3I would have thought (and done) the same thing as the players.
* If Ion Weapons shoot streams of ionized particles at something (as defined in SW), they should be pretty trivial to shield against, and they shouldn't be as effective as they are in SW. In the 3I, gas scooping from Gas Giants is a standard way of refueling. I'm not going to get into if scooping is really possible - it's a thing in Traveller so we'll say it just works. Gas Giants are infamous for very powerful fields of ionized particles, as well as electrical storms and similar ionized hazard (lightning is very powerful btw). However, there appears to be no real hazards like this to scooping from Gas Giants - it's considered a sane and reasonably routine thing to do and many ships do it. This would suggest that 3I starships are all pretty heavily shielded as a standard so you'd need some really powerful Ion guns to do anything.
Possible balancing factors and their implications:
1) Ion Guns are Short-Ranged. People would make ion missiles and ion torpedoes. The missile cruiser would once again reign supreme or at least be a serious threat. As would "fighters" - fighters here being the smallest practical ship able to carry ion torpedoes. 3I battleships would likely be dethroned by the smallest ship able to fire powerful ion torpedoes. Meanwhile "aircraft carriers" would exist again, even if their "fighters" are like 200DT ships.
2) Ion Guns aren't as strong as lasers. As I mentioned above with the shielding that would be standard on Traveller ships, so if Ion guns are weak, most ships would be immune to them and they'd be a curiosity, not a weapon. They might be used to disable really light ships that aren't intended to refuel in gas giants like gigs or something. If they scale, then you have the problems in #1 again.
3) Ion Guns require more power than lasers; much more but if fed that much power, they're powerful. Mission killed is mission killed. If it's as efficient or nearly as efficient as a meson gun at killing stuff, then Ion Guns become the new spinal mount. This might result in something crazy/silly like Warhammer 40k or something - ships disable each other with Ion Cannons then marines swarm on board the disabled ship to fight it out - ships are very expensive and captured ships can be added to your fleet.
4) Ion Guns are strong enough to get past standard hull hardening but reinforced shielding is effective against them. I'm a bit leery on this. It sounds like the easiest explanation, but lightning in gas giants is pretty strong and lightning is pretty destructive yet even today most airplanes are pretty much immune to it. I guess you might do this making the smallest practical ion gun to be the spinal mount of a cruiser or something, but again, if they're so effective, they're going to displace large numbers of other weapons.