Is it permissible to supplicate with "O Allah, honor Islam and Muslims," taking into consideration that Islam is already honored and will remain so?

There is no objection to supplicating with the aforementioned wording, and it does not mean that Islam is abased. Truth is never abased, even if it is overcome. Allah's saying, "It is He who sent His Messenger with guidance and the religion of truth to manifest it over all religion, even if the polytheists dislike it," indicates the might of Islam. The meaning of might here is: prevalence, empowerment, victory, and support, as in the Prophet's (PBUH) saying, "Islam will remain mighty until twelve caliphs, all from Quraysh." A supplication similar in meaning to this was narrated from the Prophet (PBUH): "O Allah, grant might to Islam through the one of these two men whom You love more: Abu Jahl or Omar ibn Al-Khattab." And His (Allah's) saying "O Allah, grant might to Islam" means: strengthen it, grant it victory, and make it dominant over disbelief.