So then because thou art lukewarm, and neither cold nor hot, I will spew thee out of my mouth. (Revelation 3:16)
Either the content is important enough to include, or don’t include it. Don’t make those using your content go searching for it, or worse, chasing potentially broken links. Instead, include it directly and link to the source or provide a footnote.
This is also the reason that only aggregate dependencies are listed in the kegdex file. Any other link is simply reference relationship. Such content should either be so trivial that it can be included in a footnote or explicit URL (which are only allowed in list items in KEGML), or so important that it should be copied directly into the node (or a separate content node of its own).
This is why services like StackExchange, Wikipedia, Quora, and others require that the content to which someone might simply link be quoted and included in the “response” as well. It is likely that the source of that information might go away eventually. This has also been de rigueur for academic writing for several decades.