Thou and you are two different words. Thou is the nominative which conjugates to thee and thine. More importantly, thou is the English counterpart to the tu you find in Romance languages. Thou was acutally the singular form, and ye the plural, also matching the distinction you find in Romance languages. Thou to thee is the relationship of ye to you. That is, ye was the nominative and you was the dative and accusative. Though the spelling of thou and you make them look like they're a pair, or one comes directly from the other, this isn't actually the case.

Graphically, the shift from thorn <þ> to <y> actually went through a sort of roundabout change by way of <ƿ> (in written form at least) before really representing <y>. More significantly though, the reason behind it had less to do with natural changes going on in the orthography than it did technological limitations in early printing.

Regarding confusion, due to the differences in function between "the" and "ye", the <ye> of <ye olde>-style constructions could not possibly be confused for "ye" meaning "you". It would be agrammatical to a speaker of Middle English. Context would make it immediately apparent what it was that a person was reading, and anyway, the <th> digraph had become common enough by then.

Adding to that, spelling was hardly standardised, so having wildly different spellings of common words would not have been such an issue.

Remember that you're reading a language you already speak so you're not likely to confuse the word that's on the page since you already have a good idea what it should be. So anyway, no, not really, you wouldn't have the kind of issue you're suggesting.