So I reboot into CWm and "wipe data and factory reset" before flashing the rom.
First boot took a long while as usual but the nook was very sluggish even after booting.
Also ,astonishingly, I had GAPPS(!) installed on this ROM even though I precisely remember not having flashed the gapps package in CWM.
I double checked the md5 hash and re-flashed the ROM but to no avail. Still same issues.
Flummoxed I started searching if Google had suddenly started allowing CM to include gapps with the ROM. No luck there.
Then I saw eyeballer's comment here. Worked like a charm.
So basically, when in doubt, format /system
Post formatting /system and another fresh install things go back to normal. No ghost of gapps. No extra sluggishness. All cool.
Now, this solution worked for me and hence I'd recommend it to anyone in a fix but I can't seem to be able to find a specific reasong for such behavior apart from a broken zip.