1. Why has the level in the pipe gone down?
You have removed some magma from the pipe. Thought your system is closed, some magma was required to fill/prime it, which was taken from the pipe. That caused the magma level to fall. Eventually the pipe will refill itself to its original level. This may cause it to overflow if magma flows out of your system into an already full pipe.
2. Have I just pressurised the entire magma pipe?
If there exists a solid path from the outlet of your pump to the pipe, then the entire pipe will be pressurized to the level of the output of the pump.
1. Are there any issues with pumping magma through a pump stack?
Only that the pumps should not contain any wooden parts. Other materials seem to be safe - pumps don't seem to need magma-safe materials so long as the passable input square of the pump is not itself immersed in magma, which it does not need to be in order to pump.
2. The magma should be pressured at the top of the stack, correct?
Yes, the magma will pressurize to the output level of the last pump.
3. How many pumps can I reasonably place at a magma pipe that it does not lower the magma level?
None. Pumping any magma from the pipe will lower the magma level. The pipe will eventually refill to its original level.