House from the early 1900s that at some point got an indoor toilet, with plumbing added afterward and holes made for these in the basement (likely).

The problem: from the hole, you can feel stale air flowing in. Not damp/mold or similar, but it smells like floor/under-layer.. old debris.

I would like to seal it and first thought of lime mortar similar to the rest of the walls. Then I became uncertain about the pipes and what's inside. Is it a very bad idea to close off access to such pipes and connections that you can see a bit in?

How would you have done it? Old brick wall with exposed pipes in a basement showing cracked plaster around an opening.
Cracked wall reveals pipes and wiring in a basement, with debris scattered around; part of an early 1900s house discussion on airflow and sealing.
Underground plumbing with exposed pipes and wiring, showing signs of natural debris and potential ventilation issues in a basement area.
 
Yes, copper and cement are not a good combination. It appears to be connections on the heating system that have a limited lifespan. However, a leak on them might not be dangerous since there is only a limited amount of water in the heating system.

One thought I had was to fill with lecakulor and then an even layer of foam that you can then plaster over. This way, you'll have something that's easy to "dismantle" if you need to repair something in the future.
 
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