No, the web interface shows the package version, which of course doesn't change when you replace the cgminer binary.
Looking very much forward to updated cgminer for my S3+, keep up the solid work, ck & Kano!
S2 is in the works now, the S3 is after that and will be more effort than the S1 and S2 combined

That's what I figured, but wanted to double check. Thanks for including the API version check instructions, makes me feel better to verify that I did it correctly.
Good luck with S2 and S3, sorry to hear S3 is going to be so much work, hopefully it's worth it!