I had the same question years ago when I got serious about Home Theater; clocking cables are 75-ohm digital, just with BNC connectors as well all know. When i asked this question of some people I trusted, I was told that despite the fact it's just 1s and 0s heading down the line with a pure digital signal, that whether the cable is certified as a true 75-ohm cable, whether the signal goes out on the cable (and stays) free from aberrations, noise, reflection, etc...all makes a difference. In short they were right. Just like routing Dolby Digital, DTS, or PCM down a digital cable, with clock pulse info, the answer is the same; it definitely matters that you use a good quality BNC terminated digital cable. I cannot speak to whether one manufacturers cable "Y" is better than their cable "X" just because it is a step up in the line from a marketing and price point of view but your ears will tell you (after the clock and cable are properly broken in), which one gives better results. This will depend upon that manufacturer's cables and whether (for digital) there is actually something better about the cable itself. I've done upgrades at various points within cable lines I've used in the past; in some cases the results were very obvious and substantial (broader/deeper sound stage and/or better precision of imaging, etc..) and in other cases, the differences were only slightly noticeable. Depends upon the cable line and true diffs between the steps in the line-up as I mentioned before.
A short while ago, I did do a clock cable upgrade in my system and take a step up in the Kubala line; my prior cable was already of extremely good quality and the system sounded great with it over a 2+ year period. The difference was beyond my expectations and to a surprising level. Again, depends upon the cables you choose, who makes them, etc...