The convention generally follows that which we see for minor key signatures. There is not a 1 to 1 relationship of key signature to root, rather, the key signature is there to tell us what notes exist in the scale. Then, we use the music itself to figure out where the root is.
If you were writing in D phrygian, for example, would you have two sharps in the key signature and then naturalize all Fs and Cs while flatting the Bs and Es? I should hope not, that would be confusing as all heck as far as I'm concerned. You would write two flats and be done with it.
And yes, it's true, writing a natural key signature for G mixolydian could easily be confused for C major. OR for A minor. OR for F lydian, D dorian, or B locrian. We already have this convention for major and minor (i.e. Ionian and Aeolian), it's just that most people don't realize there are other possibilities. When they start seeing that in the music, they'll realize soon enough.
The "church modes" as we know them, are the ones with the most background in western tonality, so I consider this convention to apply primarily to them. When you're talking about scales like super locrian or lydian dominant, there exists far less precedent. These most commonly occur in jazz music, where the key signature (if any) is most likely going to be a simple representation of overall major or minor key. The key signature matters less in this situation, since the scale/mode is going to be changing with the chords every bar or so anyway.
Similarly, when you have scales that are less common in western common practice, like the Arabic scale, Ukrainian minor, what have you; there is little history of these being notated according to western traditional rules. In many cases the musical tradition would not be notated, or there would be an alternate system of notation.
In contrast, the common usage of modes like mixolydian or dorian would be in a harmonically inactive setting. This lends itself to using one key signature for the entirety of the piece. If you're trying to notate non-western-traditional music, feel free to make up your own rules, but if you're using these types of scales in a jazz or highly harmonically active context, your key signature is probably not going to be directly related (should it exist at all).