I'm seeing the same thing. There is no problem showing S/MIME encryption and signing status with 'normal' accounts, or in Local Folders. Therefore I'm fairly certain it's related to Owl. So contacting them is the right thing to do.

Thanks for the check, I'll leave this open until I get an answer from Beonex or find a way to solve the issue itself.

I have this issue as well and wrote to Beonex support for Owl. They responded that, as of this writing, they do not officially support encrypted email for Exchange accounts, citing "the API structure of Thunderbird, which often does not allow us to re-use parts of the Thunderbird code".

I think their statements about encryption not being supported, and not bearing responsibility for dissidents using it is just a lame excuse. And it is contradicted by the statement you got about the lack of Thunderbird APIs. Nobody expects Owl to actually do the encryption, but they should provide the GUI so that encryption can be set up for Owl accounts in the first place. Wrt the missing S/MIME button, the corresponding button for OpenPGP encryption works perfectly fine with Owl, so I don't see any reason why this shouldn't work for S/MIME. It seems they are either unable, or unwilling to fix this. Since Owl is a paid product, the lack of proper encryption support does not sweeten the deal.