Yeah, the exceptions will almost always be there, no matter how hard you try to standardize a rule. We also have two characters in Romanian pronounced the same (Â and Î), but there are simple rules governing which one should be used instead of the other (Î at the beginning and end of words, Â everywhere else).
Oh, our rules for <ů> and <ú> are also supposed to be simple - <ů> in the middle or end of word (roots), <ú> at the beginning. But once you dwell deeper, you realize it's not that simple - you have to watch out for prefixes, so for example you have 'účast' (participation) and 'neúčast' (non-participation, absence) - <ú> is there in the middle of the word. It's fairly obvious in this example since 'ne' is about the most used prefix in Czech, but there are cases in which it is very difficult to decide.
And there are also pretty absurd examples of exceptions: foreign words, even those most people don't recognize as such, are never written with <ů> (unless, I was told, the word has been really profoundly integrated into our language - which is about as arbitrary as you can get and there is no rule that can help you there).
So for example there is 'kúra' (a type of medical treatment) and 'kůra' (cortex, the surface layer of a tree). It sounds the same, but it's written differently.
Ignorance is bliss, in some cases

It is said that foreigners generally learn how to speak Czech pretty fast (they almost never learn the high form of the language but the common Czech, which is sometimes pretty funny), but learning how to
write Czech properly is difficult even for many native speakers.