Does a bibliography-only citation count like a regular citation for the author? There is a very nice open source toolbox for Matlab which I have used for proof of concept. However, the real implementations in my field are almost always done in C++. I really like to give credit to those behind aforementioned toolbox and I have two of ways of doing so. 

One is to add a sentence in the paper similar to:


  one can achieve this using toolbox Foo (Foosmith 2015)


I’m not really fond of this approach because not only does it occupy valuable space, but also somehow states the very obvious (somehow an insult to the intelligence of the readers). 

My second approach is not to cite them in the paper but add them in the bibliography (can be done with \nocite{} in LaTeX). My question is, if I follow this path, would it count as a citation for the creator of this toolbox? If it matters, my paper is to be submitted to an IEEE conference.
In the main text, you could also mention the authors by explicitly stating what their tool helped you with, for example:


  Our approach was projected/tested/verified using toolbox Foo (Foosmith 2015) and later ported to C++ for performance measurements.


Apart from thanking the authors, this could also be interesting for the reader.

As the other answers mentioned, a bibliography-only citation counts the same as a regular citation, but such a citation is quite unusual and generally not recommended.