Hello,
I have this same issue and after some research i have determined that it is a problem with how wminput uses the blue-tooth adapter.
Here is an old Ticket for wminput that explains the problem a little better.
http://abstrakraft.org/cwiid/ticket/71
Using -d appears to be what causes the issue.
When I remove the -d flag I can ssh into my raspberry pi however with -d enabled I cannot.
HOWEVER:
By removing -d you cannot add a wiimote after the system has started.
You can connect them when the retropie screen appears by pressing 1 and 2.