The solution is simple enough: look at the companies books, if money is leaving the country, duty is charged unless it can be accounted for by something else (like the existing duty on physical goods).

IRS: Hey Google, you said you made this much money, so you owe us tax.

Google: No, see, here we paid it to Google Ireland as IP license fees, so we in fact made $0

IRS: Great, you owe us duty on that payment