I suppose we can't now ask the scientists and other intellectuals and scholars working in Catholic and Protestant universities in Europe - or the scientists of the Islamic "Golden Age" - whether they truly believed in God.
Isaac Newton was well known for his theological writings even as he was recognized as the greatest mathematical mind of his age. You can't ask him, but I think his writings speak on his behalf.
I have worked with a number of scientist-believers. One of my former experimental colleagues was also a member of my church.