Well, it is indeed troubling if Vulcans actually pray. That is not a logical thing to do. Another reason to dislike Voyager, I guess.
What do you think the entire "Search for Spock" ended up meaning? The ritual at the end of STIII was strict spirituality/faith, without a shred of science involved in the act.
In TOS, Kirk, McCoy, Uhura and Scott have all made religious references (Christianity), and not as loose slang/expression, either. No episode was stronger in providing this proof than "Bread and Circuses"
where Uhura and Kirk openly acknowledged God/Christ's existence, and this was an episode written by Roddenberry (along with Coon and Kneubuhl) while Roddenberry was involved with the series.
Spiritual belief exists in the ST universe across all eras, which calls into question the motives of various ST books which try to paint the franchise with revisionist brush, as though religious belief was nowhere to be seen in ST since "The Cage."