Translation:The subjects that he chose were too hard.
"The subjects which he chose were too difficult." My translation is identical in meaning. "That" or "which" can be the object of the relative clause. In English, you can even omit "that" or "which" and it would still be correct. "The subjects he chose were too hard."
As a native (American) English speaker, I would say that "that" and "which" are not interchangeable if you want to speak with perfectly correct grammar. "Which" begins a non-restrictive (non-essential) clause, and "that" begins a restrictive clause. Examples: "The dog that ate my homework is over there," in contrast to, "The dog, which just ate my homework, is over there." In the first sentence, it is implied that we are specifically looking for the dog that ate my homework, maybe to punish him, and we have to know which dog was the one that ate the homework. In the second sentence, I am adding some non-essential information about the dog eating my homework, but the real point of the sentence is just to say that the dog is over there. In the English translation of our Czech sentence here, you would need a comma if it said "which:" "The subjects, which he chose, were too difficult." To me, that means that the fact that he chose the subjects for himself is interesting but not essential to know. So the translation of the Czech sentence should be, "The subjects that he chose were too hard" or simply, "The subjects he chose were too hard." :)
Woudln't past perfect be preferable here in the English translation? The subjects he HAD chosen were too hard? Seems like a rather clear example of a time sequence.