Why is a message not printed as seen in mutt?
Why is a message not caught by spam defense when piped to?
You might suffer from bad values for print_decode and pipe_decode. If you set them to "yes", then mutt sends the rendered message as you see it to the external cmd. For printing this is often (but not always!) desired, for spam defense it is never good! Make sure you turn it to "no" before you feed your spam watch dog, and reset for "regular" use. See also display_filter.
How to launch a browser with text links in plain text but encoded eMails?
urlview comes packaged with mutt, see contrib dir for code and help. Basically you pipe the message to urlview. But there are some boobytraps to avoid, see previous faq, and also /Attachment.
Is there any way to search encoded messages like quoted-printable ones?
set thorough_search=yes so Mutt decodes mails before searching.