Mawdrigen said:
Ah should point out two things.
My traveller sertting is not otu, and the two major powers are at war and quite happy to raid each others shipping.
For inspiration, I'd consider piracy in the age of sail, and commerce raiding by German surface ships in WW2 and WW2.
In the former, merchant ships carried guns just as capable as those on warships, just not as many because they needed more space for cargo. Pirates could count on a bit of a fight from a merchant ship, and navies patrolled the seas looking for pirates. Of course, in those days nobody had radios so naval patrols couldn't home in on the evidence of the latest attack.
In WW1 and WW2, primarily due to the threat from U-boats, merchants usually travelled in convoys. They sometimes carried one modest size gun, again to deter surface attack by U-boats, although at least one captain got carried away when being attacked on the surface by night, thought he was up against an auxiliary cruiser, and tried to fight back. He got a shock when he found he was challenging the pocket battleship
Admiral Scheer.

Auxiliary cruisers were ex-merchant ships fitted out with a full complement of naval artillery, albeit older guns with second rate fire control. German cruisers would try to take British merchants by surprise; British cruiser would try to take German cruisers by surprise.
Back to Traveller, then, and depending on which model you follow - and how likely help is likely to arrive - merchants might very well have the same sort of weapons as navies, just less of it. For sensitive weapons such as particle beams or even nukes, the ship might be on a government contract, the weapons are fitted by the government, and there's a naval gunnery team on board to use them. Also present are marines, partly as additional defence against pirate boarders and partly to discourage unauthorised use of the weapons.
Or there might be well escorted convoys. Depending on the government's attitude, freighters might be allowed to travel alone and unescorted, at their own risk; or departure without being part of a convoy might be forbidden. Merchants definitely don't get access to special weapons; if you want the protection of heavy artillery then you go with an escorted convoy.
And if the players are the raiders, one risk they have to consider is that what appears to be an innocent freighter may have a bay-mounted weapon in its cargo hold and a platoon of marines in the passenger cabins. The words "Q-ship" and "Oh ****!" should be heard in the next few minutes.
