When I connect the emerald pipe to farm hatch all filter settings are bypassed.

Is the pipe connected to the bottom of the hatch? The hatch automatically output to a pipe at the bottom of it, so you could have used for example gold pipe instead. Why do you need to filter the output? If the Farm is outputing anything it is because it doesn't need the resource.

@SandGrainOne - I still think, no matter that, that filtered extraction pipes should respect their filters upon item extraction attempt. What do you think?

In this case the pipe is technically speaking not extracting anything. The hatch is activaly pushing items into the pipe. But I understand that it this might be confusing. Not sure what the best solution would be.

I don't like machines that automatically output resources because I think that is something the logistics should take care of, but that is a different story.