Why is "co je to" not good? When does word order matter, or what rules are there as to it?
Co je to? is completely fine and accepted.
Does the word order here effect the emphasis? Like, "what IS that?" vs. "what is THAT?"
In this case not too much.
I'm used to hearing people say "Co to je?" Is that the most common word order for this phrase?
Both Co to je? and Co je to? are very common.