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If you then don't find it, give https://developer.valvesoftware.com/wiki/Flex_animation a read. Also, yes, you'll have to de-compile the model first, and Crowbar is recommended for that.
A short guide is to import the SMD (or DMX if you have a DMX of the model), then use a program to add blend shapes or something (in Blender they are called Shape Keys, I think).
Then if you export as SMD, you'll get the SMD and a VTA (so make sure to keep the original SMD backed up), and then you can use the VTA with both SMD and DMX models, if you use $FlexFile in the $Model statement (the link covers it).
If you export as DMX, however, the flexes will already be embedded in the DMX model, ready for use with $Model, $Body and even $BodyGroup. Just try not to have under-scores in the shape key names for DMX flexes, as that'll cause problems if you don't know what that does.