As the kings of Bohemia and Hungary were almost always Habsburgs after 1526, It wouldn't make much difference.
Actually, the I was pondering the whole situation in Bohemia and Hungary in EU last night, and I realized that the game really needs some reworking in this area. Here are the problems and my suggestions on what could be done:
1. As I stated before, from 1490 to 1526 (and even after, although the throne of Hungary was in dispute after the Turkish invasion), Bohemia and Hungary were united under the same king. This can be simulated in the game in three ways: a) Bohemia and Hungary are united. As Vladislas/Ulaszlo was king of Bohemia first (from 1471), the game should simulate that Bohemia had recently annexed Hungary. Thus the only national provinces for Bohemia-Hungary should be on the Bohemian territories, and Hungary should have residual nationalism, as any nation conquered/annexed two years previously would have (which is quite historically accurate; Ulaszlo faced continual dissatisfaction among the nobles who elected him, and there was a major peasant revolt in 1514), and may break free at a later time under its own kings (as it did to a point after 1526). b) Bohemia and Hungary are separate, but Hungary is Bohemia's vassal. This option would make it easier for Austria to eventually annex either or both of these countries, and would also allow Hungary to become completely independent later (as part of it did after 1526 under the Princes of Transylvania). c) Bohemia and Hungary are separate, and only allied to each other hand have a mutual royal marriage. An OK idea, but I don't think it would do justice to the situation.
2. Vladislas was a member of Poland's royal family; in fact, he was the placed upon the throne of Bohemia by his father Kazimierz IV, who died in 1492. Thus the thrones of Bohemia and Poland were closely allied; this should be indicated in the game by at least a royal marriage and quite possibly as an alliance.
3. Bohemia's religious situation was unique in Europe in 1492. Early in the 1400s, the Bohemian Jan Hus preached the Catholic Church was in need of reform, made proposals about said reforms (many of which anticipated later Protestant ideas), and was burned at the stake in 1415 for his troubles. However, his ideas caught on in Bohemia, and for all intents and purposes Bohemia was a Protestant state after 1415. Later Catholic kings would attempt to bring the Bohemians back into line with Rome, but the best that could ever be done (until the Counter-Reformation, that is) were temporary compromises. Bohemia even elected a Hussite king, George Podiebrad, in defiance of the Catholics; he died only in 1471. Thus, in my opinion, the national provinces of Bohemia (excepting Silesia) should start the game as Protestant. Of course, no ruler at the beginning of the game can be tolerant of Protestants, meaning that Bohemia will be difficult to rule effectively. This too reflects history; Bohemia was notoriously hard to manage and was the scene of many notable revolts, most due to Catholic rulers trying to suppress the Hussite movement.
