I think what’s most important is to consider the balance of what happens in the actual game. I don’t think every unit necessarily has to have a counter (depending on the unit), but should -at least- have something that goes on-par with it (even if it’s in a different way), whether it’s a single ship or a composition of ships. What happens in reality is people use unit compositions – now, how many different ships are in that composition can vary, sometimes you can have a composition composed of a single ship. And you don’t have to just consider each individual unit. You can also consider how many ships are allowed in the fleet, a dyanmic which Homeworld uses uniquely by limiting numbers of a ship type in some cases and in other cases the number of individual ships. You’d be hard pressed to counter 4 Battlecruisers once they’re out with Medium unit cap settings, but the number of them is limited so there is a limit to how many resources can be invested in them instead of other units, which gives a chance for opposing fleets to make enough numbers of different units to deal with the BCs, and each BC lost is a pretty big loss on its fleet’s side. There are also other ways to balance that aren’t based upon individual unit stats, such as production time nerfs/buffs and nerfs/buffs to counters of the unit’s counters.
You can still maintain asymmetric balance with this. For instance, look at the Hig Interceptor-Kush Missile Destroyer-Hig Ion Frigate relationship. The Missile Destroyer will do well against Fighters, but Hig doesn’t have a Missile Destroyer to go toe-to-toe with the Kush Missile Destroyer. They do, however, have their own Ion Frigs, which do pretty well against Missile Destroyers. In turn, the Kush player might use Attack Bombers to counter the Hig Ion Frigates. In this case, you have an interesting dynamic where you have Interceptor/Ion Frigate vs Missile Destroyer/Bomber. It may be a balanced composition matchup (just going with these units by simple logic here for demonstrative purposes, I don’t know how these compositions actually fare against each other as I haven’t really encountered the matchup of them), but they’re both strong in their own ways.
Of course, we know that the Kush player can also build their own version of Interceptors and Ion Frigates, but I consider Homeworld to be a semi-asymmetric game, compared to something like the fully-asymmetric SC2 where no units from the different races are the same. Each race in Homeworld might have similar options (Vaygr perhaps having the least amount of similar options, but still some), but each race also has options unique to them which increases diversity by providing different tools to deal with different compositions.
What needs to be watched out for, however, is that the balance isn’t majorly based upon game stage, as forcing players to be defensive for a long period of time until they can get the proper research out is a recipe for frustration. Missile Destroyers are fairly high up the tech tree, but thankfully Kush also has Scouts, Interceptors, Light Corvettes, Multi-Gun Corvettes, and Drone Frigates to deal with Fighters, with Attack Bombers (to an extent), Heavy Corvettes, and Assault Frigates to deal with Corvettes. Having plenty of diverse options each with their own strengths and weaknesses that are balanced with opposing options at all stages of the game is what allows asymmetric balance to be fun.
What happens when this isn’t followed is frustration. See: HMF spam. It’s considered by many to be too difficult to stop HMF spam once it’s started because at that stage, when production rates are considered, the counter options to HMFs often have trouble actually stopping HMFs in time. Thankfully, it seems like this is being addressed by the changes being looked at.
