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  to evaluate XY (...)
in your paper, where
 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).