I've been thinking about how common ion cannons would be on law-abiding (or pretending to be law-abiding) civilian vessels, i.e ships that aren't operated by the Imperial military, local security or licenced bounty hunters.. Based on the information in the rulebooks, there's no legal barrier to a civilian ship carrying ion cannons; they're not listed as Restricted on the price list. That's fine as a letter-of-the-law view, but I think a lot of Imperial and security personnel would view ion weapons on a civilian ship as... suspicious.

I can see two ways such weapons would be viewed:

1) If civilians want to mount ion weapons rather than lasers or blasters on their ships, so much the better. It's preferable for semi- or un-trained civilians to be using non-lethal weapons rather than blasting away with quad-lasers ay time they get spooked.

2) There's no good reason for a civilian ship to mount ion weapons. If a law-abiding ship needs to open fire, then it must be under attack from pirates, Rebel terrorists or some other breed of scum. In that case, the civilian ship will be trying to escape, not take prisoners, and their attackers are more likely to break off the attack if met with deadly force. The only reason to mount ion weapons is to take another ship intact, which a civilian ship would never want or need to do - that sort of thing should be left to the proper authorities.

I tend toward the second view, at least while wearing my GM's Imperial officer cap - Ion weapons are, strictly, legal, but invite further scrutiny and could lead to trumped-up charges under another pretext - but I'd be interested to hear other people's views.

I'm not as versed in GM terms, but as a long time Star Wars nerd, I'd say that the Empire would be suspicious of any kind of weaponry on a strictly civilian craft that isn't traveling through dangerous space. If the ship is being checked, more than likely the Empire takes note of the weapons and would find Ion Weapons to be just as suspicious in most cases. However, I believe most laser weaponry in the Star Wars universe is cheaper (citation needed), so they'd probably ask the crew why they'd pay the extra money to get specifically Ion weapons unless they're part of a corporation who make it standard, have a guild mandate, or some other reason (i.e. maybe the PC's are posing as missionaries who would believe in nonviolence, or that the weapons were installed with the ship when it was found/bought and the crew never changed it).

Ultimately, I'd say that whichever one you choose will mostly come down to what needs to happen for the plot. If it's not supposed to be a big thing, then maybe the checkpoint just takes note of the Ion systems and then sends them on their way. If you are trying to make it tough for them, make the Empire suspicious and make them lie/bluff/talk their way through it.

Would you be more suspicious of a person claiming self-defense packing a taser than one with a pistol? I would not, so I go with option 1.

In ye olde WEG days they would deep dive stuff like this.

Their take was to legally mount weapons required a weapons load out permit. What the Empire would allow depended on what, how much, and where you did business. So like a ship that did a lot of business in the outer rim could easily justify a pair of quads and a concussion missile launcher, a ship that stuck to the core would have trouble mounting a single blaster cannon.

On the topic of ion cannons the opinion was very much your option 1. Nonlethal weapons were easier to justify. But that was in context. A medium freighter mounting a few light ion cannons was not a huge question. The same ship mounting a few heavy laser cannons, a few ion cannons, a tractor beam, upgraded armor, and a cotterdam universal airlock....might have trouble getting a permit.