No, that should not matter. There could be various reasons:
1. Wrong reference to the fonts in either CSS, XHTML or OPF
2. Font is obfuscated in a non-standard manner
3. the font is not included in the ePUB
4. the OS/2 Version property of the font is not 3 but higher or auto.
Number 4 is the most tricky one. You can check (and adapt) the OS/2 version property via FontForge.
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