Regarding #1: True, it seems that there are some countries like the UK [1] have thresholds, but others don't seem to have any (eg Ireland [2]). No matter if they exist or not, there are still companies that have large EU based turnover (Github, 37signals), and they too don't charge VAT.
Regarding #2: I agree. It's not that I want to convince anyone to start charging VAT. I'm simply trying to understand why this directive exists and why no one seems to care :-).
[1] http://www.hmrc.gov.uk/vat/start/register/when-to-register.h...
[2] "(g) A non-established person supplying taxable goods or services in the State is obliged to register and account for VAT irrespective of the level of turnover." http://www.revenue.ie/en/tax/vat/registration/index.html#reg...