Does EBSCO's "Peer Review" search filter filter out junk journals?
Yes.
However, keep in mind the various (read: broad) definitions of what peer reviewed means. EBSCO uses following definitions:

Blind Peer Reviewed - (or Double Blind Peer Reviewed) - Articles appearing in a journal are sent outside of the journal's publishing or sponsoring organization for review by external reviewer(s), whereby the either author's identity or the reviewers' identity is unknown.
Editorial Board Peer Review - articles appearing in a journal are reviewed by an internal board of editors, not solely by one editor. The author's identity may be known or unknown.
Expert Peer Review - articles appearing in a journal are reviewed by experts (either internal or external to the journal) whose credentials are known and who are experts within the subject matter of the article under review. The author's identity may be known or unknown.

According to EBSCO, you can also restrict your search to peer reviewed articles by suffixing your query with AND RV Y.