On the upside, most of the older SMX ships have a lot of weapons which allows them to have superior firing arcs to most KFY ships, whom often focus on powerful frontal weaponry. That offsets their maneuvrability disadvantage.
I'd think that the older SMX ships probably make great second-line troops, set to garrison systems and interact closer to gravity wells. Defensively, most of their disadvantage are put aside, and they still have very large complements of crew, slaves and battlepods.
When you consider that, the best circumstances for SMX battlegroups is when they close distance and penetrate enemy formations, or are penetrated by other ships. Rather than lose organization, their lot improves because it allows many of their ships to be surrounded by common targets, thus allowing them all to use the weapons on more than just their fore.
One big advantage the SMX had before was their tunneling positron cannons, whom could defeat shield technology of anything built or refited before YE 29. At YE 30 and beyond, shield technology caught up with the vessels latest built, or with refitted shield systems, and thus making the tunneling cannons considerably less deadly (though they remain on part with most of the heavier weaponry the Star Army of Yamatai fields).