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).
Side comment:

If the hyphenated name is due to marriage, it is common to use the premarital name, especially if papers have been published before the name change. This has nothing to do with a name being too long, but rather to preserve an academic identity that has been established before the marriage. 

Assuming you don't have a pre-hyphen identity you wish to hang on to, I wouldn't worry about it too much. I also have a hyphenated name and as far as I can tell, the only difference it makes is that my name is more likely to be abbreviated on posters, slides or SO usernames.