The use of SHA1 with HMAC, inside as well as outside of the context of SSL is still acceptable, yes. Even against a nation state attacker. The reason attacks on HMAC(k,m)~=SHA1(k||SHA1(k||m)) are much more difficult than general collision attacks is that as an attacker you do not know the internal state of the hash function when you are trying to create a collision with m, as the secret key is input in the hash function first.

The attack vector for TLS certificates is the (asymmetric) signature which signs a plain SHA1 hash message. I'm still disappointed that after all the experiences they have had with MD5 they haven't yet started to randomize the hash in the signature (sign SHA1(random||message) instead of SHA1(message) ) which would boost the signature security to that of HMAC.

It depends how motivated your attacker is. Could someone make a lot of money if they could get SHA-1 collisions with your application?