If you clear your cache or use CCleaner you will clear webstorage, yes. I'm not sure how it works with node-webkit. I haven't really used webstorage that much, but you could always just make a simple test youself.
I'd say storing large amounts of data is relatively simple since you can use JSON for arrays, dictionaries (hash-table) and webstorage. I would have a look in the manual for more information on those subjects.