Another old topic here.... Yes, Lync traffic can be monitored in AOS 6.3:
show app lync call-cdrs
This command displays the Call Detail Record (CDR) for prioritized Lync calls in the controller.
show app lync call-quality
This command displays the call quality information for Lync voice and video calls.
show app lync client-status
This command displays details of clients that are actively using Lync.
show app lync tracebuf
This command is used to record activities of Lync data, voice, and video clients. Up to 256 entries are recorded.
show app lync traffic-control
This command displays which types of Lync sessions are recognized and prioritized by Lync ALG.
You can also see this information in the GUI by going to Monitoring section, then the various call options.