The usual practice that i've seen everyone do so far is to systematically copy the standard applications to make the customizations.
Now, copying objects has several downsides that you already stated.
In fact, the only upside for it would be, that you should have less concerns when applying the ESU, upgrading the JDE version.
Personally, i have some doubts about the validity of this "practice" of copying objects :
- If you are going to do a lot of heavy modifications, chances are that you would not benefit from the new version (from the ESU/ new JDE version you are applying), as the heavy customizations will probably be better suited to your business needs.
- If you are going to do a small customization, you would easily be able to re-apply them to the new version of modified objects from the ESU/ new JDE version.
- In fact, you're not sparing an analysis of the customized standards involved in the ESU/ new JDE version, because if you really want to benefit from the ESU, you should use the program modified by it, and not the ancient copied version of it, so you are going to have to somehow duplicate the modifications made on the standard towards the custom application.
THen again, my opinion is stricly from a theoretical point of view, because i'm not a CNC and have never witnessed the process of applying an ESU.