Are there any disadvantages of using libsodiums helpers for en-/decoding/comparision instead of the native ones? Libsodium has some helpers, which allow hexdecimal decoding, encoding and also constant-time string comparison.
So if you use the php binding libsodium-php you obviously also have the native php implementation of bin2hex and hex2bin. The libsodium replacements were introduced because the native implementations are not timing-resistent. So for sensitive data this should be used.

But if you have a library/project where you use libsodium anyway are there any disadvantages of using libsodiums functions even in places where this would not be necessary?
I mean one advantage clearly would that you can prevent to forget to use these timing-save implementations in cases where it is important if you just use it everywhere.
Functions often become timing resistant by not using short circuit evaluation. There is conceivably a small performance price to be paid by not using short circuit evaluation. 

In reality, this is probably not a bottleneck or serious concern. Edit: It also might be possible that libsodiums function is faster anyways. 

I would have commented with this, but I don't have enough rep to comment. There may be more to consider.