Some functions have replacements, others don't. Just one example: both F5 and CTRL-R in browsers do a refresh; CTRL-F5 does a hard refresh (also renews the cache); I don't think there's a non-function-key alternative for that. Losing the function keys would be a major nuisance.

The numeric keypad is useful to me too. A bit less than the function keys, perhaps, but when entering a list of numbers it works so much better. What's more: keyboards without numeric keypad also tend not to have the section with ins/del, home/end, pgup/pgdn and arrow keys; instead those keys are often arranged in cumbersome and inconsistent layouts. I use those a lot too.

I don't know in exactly which meaning you use the word "atavism", but I do know that having all these keys available, in a familiar layout, is very very useful to me.