I can gather that there can be the following reasons why an engine is disabled by default:

• it only serves a non-English language (e.g. duden.de)
• it would duplicate search results (e.g. it doesn't make sense to enable invidious when youtube is enabled)
• it doesn't work well?

But that does not explain why e.g. hoogle & pypi are enabled by default whereas npm & rubygems are disabled by default.