It would be interesting to know who, how and why determined the different ways of spelling what are very similar words.
Polish (as we know it today) was first standardised in the late 1700's, then again in 1936 (to try and unify the mess that existed as a result of the partitions and the language diverging as a result, though I think there was also some squabbling going on between rival centres of the Polish language) and then post-WW2 with the Communists introducing universal free school education.
On the other hand, it was Jan Hus who brought about many of the innovations to the (then) Bohemian language, including the use of the hacek and accents.
One thing that it's important to note is that the accent plays a different role in Polish than in Czech.