Regarding a need for armed merchants when a system can afford T type vessels, can you say... Pirates? Argh!
Seriously, though. Regarding the T types, for a decent system, standard vessel rotation will have one being fixed/updated/refitting/grounded for various reasons, one vessel working up to full status (finding out what did and didn't get fixed and fixing it), training new or old crew or on some bureaucratic assignment, while a whopping 1, count them 1, is truly available for anti-piracy work in... 1 system.
So, assuming that the above decent system has 3 T types, that means 1 is available for protection/escort/suppression work. Most likely, unless this same system has SDBs or lots of Fighters, means that the lonely T will be stuck in the parent system, only able to effectively protect only a portion of Home-World's orbitals, not including any in-system space infrastructure such as orbital extraction mines, research stations, habitats or such.
Okay, here's the point. I am a merchie out of said home system. Who protects me outside of the jump limit, or during heavy traffic, or at the other end? Armed Merchie makes sense to me.
And then there are those other systems that buy a squadron of T types. They can afford to buy, but not really maintain or properly crew them. Think small dictatorship. Or Iran in the '80s and '90s with their F-14s. Pretty to look at, but mosty hangar queens. Definitely need to have some guns aboard my merchie if I can get away with it.
And to the commercial viability of a 100t J1 merchie, well... All those great Victory ships of WW1 and Liberty ships of WWII were great for military cargos but sucked in comparison to regular freighters from a commercial standpoint. To make money off of a Liberty ship would require either a lack of regular merchant traffic or dealing in a niche market somewhere. Just look at today's world. Lots of room for big merchies plying the seas and making money. Also lots of need for little island-hopper freighters carrying smaller amounts of cargo on an as-needed basis.
So screw commercial viability. Go Navy! Maybe that same system with the 3 T types has a few 100 ton modified Scouts carrying cargo under arms as a naval merchant reserve, or maybe the IISS has a few to outfit all of the research labs and scout bases out there.
Just my Cr 0.02.