The Liferay workspace adds A LOT of magic and hidden dependencies, maybe even the node plugin nowadays. I honestly don't know.
Please note that you are not working with plain Gradle here, you are working in the Liferay environment on top of Gradle. Liferay changed a lot and added a lot of convenience for developers. Those plugins do many, many things. I have looked a couple of times into the Liferay Gradle plugin code to understand what it does and how I can work around some things that happen. We had several issues here before, things that happened only on some Windows machines, things that suddenly broke because some dependency was updated by Liferay, ...
Things like that happen, but the magic is worth it. You write some code and "magically" a jar file with a nice bnd file appears.
1) If the node variable is available in the project-wide build script, you can certainly add it there. Maybe add a comment, if you upgrade the build to a newer workspace version, to check if it is still needed. If you prefer it in the module, it is fine too. You just need to remember the error and when another module fails, add the setting. That's what we do, we have certainly 50 or more Liferay projects in git, per customer, several "toolbox projects", ... and so we have no "global" setting.
2) If you don't need it, don't add it. Please note that the theme uses node, some other modules (Fragments?) could need it too. It might be an implicit requirement. It is hard to tell without seeing your whole project, workspace versions, module types, build.gradle files, ...
In general: If you develop frontend modules, node is often useful. It makes tons of useful modules for the frontend (React, Vue, sliders, trees, ..,.) availabel AND adds several build related modules that allow you to transpile your javascript and css. It allows you to write nicer code which is then tranformed to really ugly code that all browsers understand.
We use it heavily, most of our applications are nowadays JS + Rest modules.
