I think you're misunderstanding the role of the alternatives system here. It is used to provide a simple way to use alternative programs of a similar type. The usual example, and the one used in the man page is an editor:
For example, if the text editors ed(1) and nvi(1) are both installed
on the system, the alternatives system will cause the generic name
/usr/bin/editor to refer to /usr/bin/nvi by default.
In your case,
node refers to two completely different applications.
If both are installable from the main Debian repository then chances are that one of the package maintainers will have named their executable so that it doesn't clash with the other. For example, the binary for the radio application could have been renamed to
/usr/bin/node_radio so that it doesn't clash with the Node.js
On the other hand, if you're compiling the amateur radio
node yourself, you must ensure that you either alter the compilation so that it doesn't create the same name binary or ensure that it is installed into a different path, such as
/usr/local/bin/node. If you opt for the latter, then which
node is executed when you type it at the command prompt depends on the search order in your
$PATH variable. If the wrong one is executed, you'll have to enter the full path to run it:
In any case
update-alternatives doesn't help you here.
All the above is only an example as a quick check with
apt-get download node followed by
dpkg --contents node_0.3.2-7.4_all.deb shows that the amateur radio
node is installed as
/usr/sbin/ax25-node with a link from
/usr/sbin/node to the executable. Node.js installs
/usr/bin/nodejs therefore the two will never clash.