There is an etymological link: they both derive from Latin esse "to be".
There is also a grammatical relation insofar as they share the same morphosyntactic features (tense, person, gender, number...).
One reason they appear less parallel than they are is that you chose an inverted French question structure but a normal Spanish declarative structure. French actually has a more exact analogue: c'est que.
As you note, the presence of ce here in the French and its absence in the Spanish is a difference to be expected due to Spanish's being a pro-drop language, which means that the two phrases are more or less equivalent as far as the grammatical features. The subject is before the verb in French and baked into the verb in Spanish, but present either way.
The semantics are also similar, in that c'est que, when used on its own to begin a sentence, can also be used to introduce an explanation or reason why something is the case (ex. one, ex. two).
So I'd say they're related.
If there is a divergence, it could be in the other possible meanings that the phrases have in their respective languages, and/or in the discursive value of the two phrases (register, frequency, connotation). These are both elliptical phrases that we can expect to generate a wide range of meanings, and they might not all overlap.
For example, in French, c'est que can also be used to indicate a result instead of an explanation. In "La vérité sur la vérité" (1977), Daniel Lavoie sings:
Si c'est pas payant, c'est que tu perds ton temps.
Tu perds ton temps is the result of something not being payant, not the explanation. Can es que express both relationships, too? That's a possible place of difference.
