I too have confirmed this situation. There has been an insane amount of spam getting through in the past few weeks because of the entire message being base64 encoded. One style of spam in particular always contains the text "this advertisement is presented by" and thus I want to write my own custom content filter for my account, that if "this advertisement is presented by" is contained in the body of the message, move this message to a different folder.
However, when the entire message is base64 encoded, no content filtering can be done! This has got to change in SmarterMail. SmarterTools needs to decode base64 messages in order for any content filtering rules to be applied. Without this change, base64 encoded messages completely bypass this content filtering feature.
SmarterTools, if you're listening... will you please make an update to fix this. Thank you.