You need these three lines:
hi CursorLineNr guifg=#af00af
The last line removes the highlighting of the cursor line even if cursorline is set and only highlights the cursor line number.
Your example is trying to mimic popup menu by popup window, it's complicate, I changed it to use arrow keys to scroll popup window in normal mode, it's only purpose is to show you how to change cursor in popup window:
noremap <buffer> <down> :call Omni_cursor(1)<CR>
noremap <buffer> <up> :call Omni_cursor(0)<CR>
The style of these two settings is defined by the CursorLine and CursorColumn highlight groups.
If I query these two on my Vim, I get:
CursorColumn xxx term=reverse ctermbg=242 guibg=Grey40
CursorLine xxx term=underline cterm=underline
So what we want to do is make CursorLine look more ...
I actually went with coloring the background of the line number. This way you're not interfering with syntax colors or underscores.
So basically I have this (for light background terminal)
highlight CursorLineNr ctermfg=white guifg=white ctermbg=darkgrey guibg=darkgrey cterm=bold gui=bold