I tested with the GnuPG version 2.0.30 (GPG4WIn) as well as the current 2.1.16
Windows binaries. SCdaemon was running but was unable to get exclusive card access.
Why?
The Cisco Network Manager as well as Cisco Anyconnect VPN did both gain shared
card access (they were not told to do so!). I needed both programs to get access
to the university network.

Uninstalling both Programs and restarting did resolve the issue. To find the
two offenders I used Process Explorer (Processes for all users) and used the
Find Handle or DLL functon with the search term "SCARD". All crosschecked all
Processes (except for scdaemon which sould access the card) and Services
(svchost) to be only scdaemon aswell as the services to be Windows internal.
To determine the inital issue I used
https://sourceforge.net/projects/pcsctracker/ which told me the status of my
Yubikey (as Present,InUse -> Shared Access).

As a suggestion I like to see the experimental option to change the accessmode
from exclusive to shared on the commandline (If for example the other
application cannot be uninstalled).