Question: I have a hyphenated surname, namely *Kinara-Williams.* I intend to be published in the future when I graduate and during/after my PhD.

But Kinara-Williams seems like a mouthful to cite. After reading other threads, it appears pseudonyms are frowned upon in the scientific/academic community; so what do people usually do?
Just go with the preferred one?

Answer: 
As other have commented, the length of your hyphenated surname is not problematic at all: keep it and don't worry.

Fun fact. Uh, well, it took me years to discover that [Lennard-Jones](https://en.wikipedia.org/wiki/Lennard-Jones_potential) was actually just one person and not two, and that the [Hanbury-Brown-Twiss](https://en.wikipedia.org/wiki/Hanbury_Brown_and_Twiss_effect) experiment was devised by two people and not three, Hanbury Brown (no hyphen) and Twiss. For [Jaynes-Cummings](https://en.wikipedia.org/wiki/Jaynes%E2%80%93Cummings_model), instead, I tought they were two and they were actually two - amazing! But I would count this as a minor inconvenience, which actually taught me not to make assumptions on surnames (and, as suggested by E.P., [this popular page](http://www.kalzumeus.com/2010/06/17/falsehoods-programmers-believe-about-names/) discusses other false assumptions).
Like others said, be consistent. Both myself and my wife's names (which are different) are longer than yours and hyphenated and it's not a problem.