Are there any disadvantages of using libsodiums helpers for en-/decoding/comparision instead of the native ones?
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.