Should I cite Papers to acknowledge usage of tools?
I would be pragmatic here. Citations are a currency in science. If the authors of a tool help your research by providing the tool to the general public, it is only fair to reference their work in the way they requested it to happen - and, certainly, citing a given reference in a paper that uses their work is not an unreasonable request. I cannot image why it would be unethical to say something like


  We have used Theano [1] to evaluate XY (...)


in your paper, where


  [1] J. Bergstra, O. Breuleux, F. Bastien, P. Lamblin, R. Pascanu, G. Desjardins, J. Turian, D. Warde-Farley and Y. Bengio. “Theano: A CPU and GPU Math Expression Compiler”. Proceedings of the Python for Scientific Computing Conference (SciPy) 2010. June 30 - July 3, Austin, TX


As to whether this is common, I would say yes. Most authors of well-known tools in my area specify a preference for how their work should be acknowledged.

If you are bothered by not having read the paper you are citing, there is a simple fix for that - read the paper, and decide for yourself whether it is worth citing in that context (but, generally, the answer will be yes).