Windows phone memory: the 64GB are partitioned, only (off the top of my head) 57 (disk!) GB are FAT32 available via USB, so 53 is about right.

As for the system memory, I guess that is RAM?
You could try on the command line /terminal app:
free
to see what the status is. the command top will show cpu and mem use, and df will show how much of the various partitions is in use.
Killing processes is easy using the command kill on regular linux, on N9 I haven't used or needed it.

The N9 behaviour you describe is very aberrant to say the least...