WinUAE is a derivative work of UAE, which is licensed under the GPL, so WinUAE can't be commercial in the closed source sense. However, the current maintainer could start charging for binaries as long as the source code is made available. Such a move would be quite atypical for an open source project such as this. Even if that did happen, there's nothing to prevent someone like me from freely distributing binaries.
Obviously, there are ways to work around GPL restrictions, but let's hope Toni, et al leaves things the way they are.
Trev