WI if the Ottoman controlled Balkans was 80-90% Muslim by 1800 how would that effect the Ottomans and Europe.
Would require serious butterflies on Ottoman actions and policies. As far as I know, Islamization was successful in only Bosnia and Albania. There were plenty of Turks in OTL Bulgaria, Northern Greece and Black Sea portions of OTL Romania but they were Turks and not conversions to Islam. Romania, Serbia, Greece were mostly Christian. Bulgaria experienced a portion of their population converting to Islam, known today as Pomaks, basically Slavic Muslims.
You would have to have an Ottoman Empire than was more successful in their conversions, have greater incentives for Christians to convert or more success in settling Turks throughout the Balkans.
Perhaps you could have a more thorough Devshirme system (boy harvest that would deplete villages of young boys to be taken back to Constantinople), a weakening of the Orthodox which was responsible for maintaining and teaching the culture.
To answer your question, even if the populations were Islamicized, they may still view themselves as not Turkish and potentially not siding with the Ottomans when nationalism comes around. But then again, maybe not. In OTL the Albanians were some of the most loyal Ottoman European subjects and last to declare independence. OTL territory of Bulgaria was, by some measurements, almost half Turkish in population and Ottomans could not retain those territories at the end of the war.