The words whys, wise, wyes sound the same but have different meanings and spellings. Why do whys, wise, wyes sound the same even though they are completely different words?
The answer is simple: whys, wise, wyes are homophones of the English language.
Plural form of why.
Having the ability to discern or judge what is true, right, or lasting; sagacious: a wise leader.
Exhibiting common sense; prudent: a wise decision.
Shrewd; crafty.
Having great learning; erudite.
Plural form of wye.
Plural form of wy.
Definitions from Wiktionary, Creative Commons Attribution/Share-Alike License, from The American Heritage® Dictionary of the English Language, 4th Edition and Wordnik.
Homophones (literally "same sound") are usually defined as words that share the same pronunciation, regardless of how they are spelled.
If they are spelled the same then they are also homographs (and homonyms); if they are spelled differently then they are also heterographs (literally "different writing").