If they were made of rubber or some such substance, they could absorb vibrations fairly well, which'd null out at least small to mediocre stuff trying to enter. Could also additionally, or alternatively, contain a bit of chakra that disperses incoming chakra/ototon? Would be even more effective, though also detrimental to wearer most likely too since they'd screw with their own chakra inside the head.
In any case, boosting the ototon with chakra wouldn't really matter in those cases, it'd still be vibrations...well, unless of course it made them so strong they blew the buds away or just shook em apart, though then again they'd be pointless to begin with since an attack that strong would deal quite a hurting regardless.
As for nulling vibrations coming their way from afar...they do and they don't.
A far bigger nuller is actually air, since to keep the same significant potency you'd have to be right up their face when releasing it, such as how Dosu did to first Lee and later Choji. Otherwise there's a very good chance the worst punch is dulled over the distance and the jutsus loses the required strength to affect them otherwise than through the ear >> and in those cases, with the buds in place, they'd be safe.
Other than that though, if you're either right up their face, or simply release such a bit attack like say a friggin nuclear bomb without the fire, destruction and radiation, then no, buds wouldn't really do anything for them except maaaaybe prevent their ear drums would getting absolutely and utterly rekt, otherwise you'd still eat the full effects of the attack cause the body would transmit the vibrations.
In the latter absurdly strong case though, it also brings up an argument against ototon users themselves; when you use a sound blast that retardedly strong, how on earth do you protect yourself much less your own ears from it? I'd like to see something a bit more logical, instead of the age old blocking own ears with chakra, cause that reeeeally should not work on the worst jutsus. At all.