You have 2 options when that happens. The damage is still 2d4+2+proficiency bonus when it's been cut in half from 2 attacks and the free prone attacks still apply to provide the party with advantage from melee attacks and possibly a net gain from situational accuracy bonuses plus wolf damage. The other option, when that isn't workable, is to keep the attack for yourself and use the bonus action for the wolf to use the help action to give advantage on an attack.One drawback that was somewhat turning me off to the class was the lack of magic attack capability. A lot of high level creatures have resistance to physical damage. That puts a huge damper on Beastmaster Damage. If they had added a means for the companion to bypass this type of resistance at higher level, the archetype would be better balanced.
Either way, I think the wolf proficiencies that add your proficency bonus as a ranger plus the bonus action help option are worth the choice. The +5 passive perception the wolf ends up getting for advantage related to sound and smell gives a passive perception of 22 at the top end and respectable to avoid ambush. It's up there with rogues and bards using expertise unless they also invest in WIS. With proficiency in stealth and pass without trace and a group check (if your DM goes for it but it is applicable RAW) in your group of 2 helping each other it only takes one to make the check for both to succeed so the duo masters stealth and detection.
Hunters have some combat benefit but the help and skill choices are a reasonable tradeoff.