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As far as I can tell none of Amazon's documentation for publishers mentions font obfuscation. (If anyone knows differently I would appreciate a link.)
I do know that neither Amazon's Kindle Previewer or the older kindlegen support input files with obfuscated fonts. Kindlegen would include the fonts without the key needed to deobfuscate them resulting in unusable fonts. Kindle Previewer will just silently strip them out. Perhaps obfuscated fonts will be handled correctly if the EPUB is instead uploaded to Amazon, but I wouldn't count on it.
Font subsetting can be problematic if not done carefully. The book rendering process can introduce characters that were not present in the original content and problems will occur if those characters are not present in the font. Two examples are automatic list numbering and ligature substitution.
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