If you have a physical legal copy of software you bought (I have original disks, manual, etc of Deluxe Paint III) then using an adf image of it in WinUAE should not put you at any risk. Even if my original disk becomes unreadable - I have a legal right to a backup and can use that - my adf images.
If people who have disk that don't work and don't care to keep them - it would be nice to offer them up for free + shipping so those of us who care could have the originals. Then we could then easily acquire working adfs and be "licensed". I never throw out old floppies or cds of stuff I purchased because obtaining a working backup/replacement is perfectly legal.
Or atleast it is for stuff we bought in the 80's and 90s. The way license agreements on new stuff read - you really don't have those rights anymore. Just like if you go to best buy and buy a PC with Windows on it. Have it a year and then lightning storm runs in on it and blows it up. Guess what - if you don't replace the burned out parts - says a mobo or processor - with an exact kind from the original OEM provider - you lose your "license" and your oem copy of windows is illegal.(Even if the parts are twice as much as buying "equivalents" on newegg or ebay.
Your OEM OS license if for that hardware in that model with those parts. That is why if you change out hardware on windows it may ask you to reactivate it once it reboots - it knows something changed and you may have lost your license.
Of course with the advent of digital delivery (ebooks, psp go, Xbox Live) we soon won't be able to buy and have physical copies of anything - it will all be licensed as service subscriptions. We won't own anything so there isn't going to be anything to go into the public domain cause companies never sold anything - they just renedered services.