@Mougatine The question is “in what context do I want to rediscover this idea?”. If it’s important that you remember C when thinking about A then they should be linked. Thinking this through is a big part of building the knowledge base.
In practice when you begin to write you should be pulling a lot of notes together and seeing what ideas you connect (in Obsidian this will most likely be through building a summary/index/MOC page). You are correct that B will provide a pathway to C at this point - question is do you only want to see the A-C connection through B.
Also - there is no such thing as a “true Zettlekasten” approach. No ultimate truth has been handed down from on high. Luhman had a personal paper based system, many others have developed and used something very similar. The fundamentals in all those systems are: 1) read with a pen in hand and make fleeting notes (that are tied to references), 2) later make permanent notes in your own words from those fleeting notes that are valuable, 3) spend time thinking about how those permanent notes connect into your existing knowledge and file them accordingly. Everything else is “what works for you”.