I don’t think the absence of afterburner hitboxes is a result of some change in internal modules strategy. Aircraft like the Shenyang F-5 and Swift F.7 do not have their afterburners modelled while the Starfighters, which came out later, have them. The F-16s and Eurofighters don’t have them while the simultaneously released MiG-29s and Sukhoys do have them. The F-5E had them when it came out and it still has them even though it has had its modules updated.
I haven’t actually checked every single jet in the game but it seems that if a non-afterburning engine has its nozzle attached directly to it, they do model it but they broke this rule on the Su-25s and also on some Soviet jets equipped with Jumo 004 derivatives. If there is an extension pipe between the engine and the nozzle, they almost always model the engine only, the L-39 being a notable exception and it seems like they tried to model just the pipe without the nozzle itself on the Etendarts. And then there are jets which kinda merge the extension pipe and nozzle into one long nozzle, such as the Vampires and the Alpha Jets, which do have them modelled.