It depends what you are publishing (and how), and how important it is to
have the support of the built-in link tools in Arbortext.
If you're using XSL to produce HTML output, and/or XSL-FO to publish
PDF, then you can do what you want. (There may be a way to do it with
FOSI too, but I never tried it so I can't say either way.) But, you
won't be able to use the standard Arbortext link/link target buttons,
and you won't be able to double-click on a link element to find its
target in the Editor window, you won't get warnings about missing or
duplicate ID's, etc.
If you can live with those limitations, then you can do what you are