Nationalism is a tough one. In Austria-Hungary for example, not all minority movements wanted independence, some wanted more rights, others a more decentralized or even federalized state. Austria-Hungary had another thing going which were rivalries between cultures within the empire, which also factored heavily in the empire's survival after the 1848 revolutions. Almost a form of "healthy" competition, really. The country was conservative, yes, but arguably not as backwards and unstable as most historybooks tell you. Nationalism, like any movement, is not black or white.
'Multicultural' and big nations are not a burden for themselves per se. They're just different and come with their own set of problemsn of course, but so does every nation. Population and size aren't even the only variables. So are geography, neighbors, history, resources etc.
My point is that it shouldn't be too punishing to be a wide nation in eu4. Or, heck, even punishing at all.