Hercules does support packet shuffling and you can use pretty much any client with it; Hercules will automatically rearrange the packets based on the client version.
About Hercules vs. rAthena, see the already existing topics:
(there's many, many more but I won't list them all)
Hercules is focused on performance and stability while rAthena is mostly focused on features and content.
The two scripting engines and database formats are similar but incompatible, this means you will need to do some conversion.