Imo the problem is that its impossible to do anything against carrier spam for most races unless they spam carriers too, not the boarding craft themselves.
I've noticed that strike craft lose their target and return back if the target ship becomes stealthed though, so all eldar and nids can sometimes counter this by boosting into the gas clouds, or by using boost+stealth stance. Also imperial navy and sm light cruisers can probably use all ahead full the f*** out of there with stealthy all ahead full skill if they notice which ship is targeted by the bobmers\boarders ahead of time (though i didn't try this myself yet). And necrons have teleport+stealth for light cruisers and pulse core for the rest.
Probably not worth it using anything other than light cruisers for imperial navy, sm and chaos until the devs fix this(unless you spam carriers yourself). Not sure about tau as i haven't played them much.