There's no reason to question the fairly straightforward etymology of indubitable - a word that has remained true to its Latin roots. It arrived in Middle English in the 15th century from Latin indubitabilis, itself a combination of "in-" ("not") and "dubitabilis" ("open to doubt or question"). "Dubitabilis" is from the verb dubitare, meaning "to doubt," which also gave us our "doubt." The word dubitable also exists in English, and of course means "questionable or doubtable," but it is fairly rare.