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.
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.
That aside, what you describe is a distinction between yod-dropping and lack thereof, and whether and where it happens is highly dialect dependent.