Is it permissible to earn money from dhikr applications with the intention of seeking Allah's pleasure, and does that affect the reward and recompense? And how can one maintain a sincere intention for Allah in such endeavors?

The lesson in righteous deeds lies in the original motive. If the motive is worldly gain, there is no reward for it. However, for one whose motive is seeking recompense and the Face of Allah, his reward is not invalidated by any worldly benefits he may attain, even if these benefits diminish it.