@Scott-Sumner is correct and mapping alt-backspace to a different function prevents the BEEP. Probably NPP capture it and fully handle it before it reaches the BEEPING control.
I got curious enough to actually open the code. This exist in NPP shortcut table:
{TEXT("SCI_UNDO"), SCI_UNDO, true, false, false, VK_Z, IDM_EDIT_UNDO},
{TEXT(""), SCI_UNDO, false, true, false, VK_BACK, 0},
Initially I thought that maybe NPP is at fault after all because ctrl-z has IDM_EDIT_UNDO which is missing from alt-backspace.
But after commenting out the alt-backspace line and compiling I had a version of NPP where alt-backspace no longer UNDO but still BEEPS.
Since ALT-xxx shortcuts are often associated with menus I guess that this is the beeping component.