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Kovid has an implementation inside calibre and Toxaris works on a stand-alone. Both worth mentioning. Search the forum.
An 3rd party online tool like squirrel isn't the optimal solutions unless you feel good with sending your files to somebody's servers.
Personally I won't see the problem fully solved until I see a tool fully capable of parsing epub and trimming every font file inside while respecting ligatures and used alternative chars. As for now this is (like many others) an optimisation step requiring manual tweaking.
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