Unlike filter inserters, that stop doing anything if a filter is not set, pumps will still pump if they are set to “Set filter” mode and the filter is empty. Making this work like it does for inserters would help a lot with circuit builds (ie. i could only set filtering signal if the destination doesn’t have the requested amount of fluid already).

Filter inserters do not work without filters even when not connected to circuit network (in "whitelist" mode). This is not the case for pumps. Because there is no separate filter pumps, they shouldn't require a filter to work by default, so "no filter" means allow any fluid, regardless of wether "no filter" is chosen manually or comes from circuit network.
Based on what was announced in FFF-393 and FFF-405, although it was not said what the default pump behaviour will be, I'm not really sure that this should be changed.
I'd suggest using Enable/Disable in your case (possibly with another pump that has filter) or just send some other fluid as filter instead of empty signal

I was thinking about disabling the pump only when the pump is in “Set filter” mode and it doesn’t have a filter set.

The real problem is that i can’t set both the filter and enable/disable through the circuit network. Right now i have two possibilities:

• manually set the filter and use my circuit to enable/disable. In this case i can’t do a meaningful blueprint (i have to manually set up filters when placing my fluid station) which is not that bad in vanilla but would cause a huge setback in an Angel/Bob run as it has tons of fluids
• set the filter using the circuit network. In this case i have no enable/disable functionality, so my LTN trains won’t depart until the train is full (which is not always a good thing with LTN, as the destination may don’t have enough space.)

In this case i have no enable/disable functionality, so my LTN trains won’t depart until the train is full (which is not always a good thing with LTN, as the destination may don’t have enough space.)

I didn't really play with LTN, but can you just set a train stop condition for the needed amount of fluid?