Changing "cube" to "kube" would just look like it's pronounced "koob" (e.g. rube, tube, lube), so we swap a minor spelling aggravation for a minor pronunciation edge case. unless you want to go full kyube but we're not putting that on the table.
Well, it would be a step backward in the right direction to go with spelling it 'kube' and pronouncing it 'koob'. That would hew to the original Greek. We'd also bring cybernetic back closer to kubernetes. And circle to kuklos. (Side note: It's another spelling "error" that we use 'y' in English to transliterate the Greek upsilon, which looks like 'Y' when capitalized, but is really a better match to 'u'. Hence, hyper and hypo instead of huper and hupo (like super and sub).)
kyube or kyoob would definitely be the way to go.
It's funny you use "tube" as an example though, as in my British accent I pronounce that as "chube", whereas I believe many Americans would use a "t" sound for that word. Not sure how you settle on a spelling in those cases.
Regional variations are available! I think the BBC would have had it pronounced tyoob. And don't Americans pronounce it "subway"?
Why would it? "u" generally doesn't follow this pattern in English after "k" any more so than it does after "c".
That aside, what you describe is a distinction between yod-dropping and lack thereof, and whether and where it happens is highly dialect dependent.