Will programs on ubuntu also access these folders?
There is default software that use them but they do not rely on them being there. For all others: Only if you tell them to. Browsers and torrent software like using "Downloads". Editors like to use "Documents". /home/$USER/
should normally be a fallback.
Mind that Desktop is fairly important as this is used as the location to show you icons on the Desktop. But even that one is not mandatory to have.
What would be the implications of adapting them for daily use or straight up deleting them?
If you delete all normal files in /home/$USER/ the system will recreate them.
There is a file responsible for setting this up:
~/.config/user-dirs.dirs
# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run.
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
#
XDG_DESKTOP_DIR="/discworld/Desktop"
XDG_DOWNLOAD_DIR="/discworld/Downloads"
XDG_TEMPLATES_DIR="/discworld/Templates"
XDG_PUBLICSHARE_DIR="/discworld/Public"
XDG_DOCUMENTS_DIR="/discworld/Documents"
XDG_MUSIC_DIR="/discworld/Music"
XDG_PICTURES_DIR="/discworld/Pictures"
XDG_VIDEOS_DIR="/discworld/Videos"
The names here also get translated to your language if you use another than the default.
There is also a command to manipulate it:
xdg-user-dirs-update --set DOWNLOAD ~/Internet
and one to view the directory it is set to:
xdg-user-dir TEMPLATES