Mmmm, dunno about the others but I can imagine Future Publishing would give permission for Amiga Format, for ages it was their pet production!
As for how to translate 'em, making PDFs isn't hard (but will result in big files), re-creating in HTML would be really tough (especially for the fancy layouts used in newer mags). Getting the original quark files and putting them to PDF would be the best solution, though it's unlikely.
As for the ads, in European mags they're a must, one of the best parts of reading old mags!
For my part if someone coordinates it I'm happy to scan some of my AFs and make PDFs.