Of course, as an academic myself, not citing the paper for some software that I used, is sloppy anyway.
So you cite the paper for every piece of software you use (ssh, Linux, gcc, etc.)?
As a member of the networking / distributed systems community, researchers certainly don't cite all of the relevant tools they use. Testbeds (like Emulab and PlanetLab) and simulators (NS2, etc.) are cited in the results section because the reader needs to understand the methodology of experimentation. However many researchers use tools created by researchers to run their experiments (CoDeploy, PLuSH, PLMAN, Stork, etc.) and these are rarely cited because they do not alter the results.
The unfortunate reality is that citations are a metric of "credit" in the academic community and the lack of citations presents a problem for researchers who build tools.