AMEN! I find notebooks a clumsy interface when you reach a certain volume of projects and am switching a design that involves nested tags. Just found out today that nested tags aren't allowed on iOS but apparently are on Windows mobile. This seems crazy as it makes what could be an awesome platform so much less versatile and customisable.
JMichael great advice! Many thanks. I was freaking out. Got a big open book exam tomorrow, all my notes were in Evernote and searches were averaging a minute. Did what you suggested and its gone back to being super quick. Running 6.0.6 on a 4 year old MBA 1.86 Ghz and 2Gb ram.