1. This should be moved to the "ideas" forum. Moddy, please!
2. I'm not sure if it's very wise to delete a WP if you don't even see it. Then again, it's in the waypointer's responsibility...
Besides, I don't know if the upcoming version will provide the possibility to delete a WP by pointing at it and if it's possible to combine these two ways of deleting WPs.
All in all, I'm wondering if the benefits of such a function would outweigh the risk of accidentally deleting a wrong WP. If you hit the del key while standing on a WP, you know exactly which one you are deleting. And if you hit the del key accidentally, you see what happens and where it happens. But if you make a typo when entering the # of a WP to delete, you don't see anything... just a thought.
Now to that backup thingy: I think the way I work is different from yours, so I don't see some points because they are simply not an issue for me. This is one of these cases where I'm not really sure what this idea would improve and why you'd need it. Mind you, I don't want to criticise here or say that it's a bad idea - I'm just not sure if I have understood your point yet. Could you explain this backup idea a bit in detail? What do you want to improve / prevent and why? Just to get the whole concept; this sounds interesting.