M-W provides the following enlightening etymology:
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.
Thomas may have doubted at first (John 20:25) but once he encountered the risen Messiah all doubt was removed (John 20:27-28). So, too, for those who follow Him today, walking by faith and not by sight (2 Cor 5:7), Yeshua is indubitably the Messiah. One day the time will come when "every knee will bow and every tongue confess" (Philippians 2:8-11) and then He will indubitably be the Messiah before all of creation.