The fishing boat was never in Russia's territorial waters. It is claimed it was briefly (less than 1 hour) within Russia's EEZ, which are part of international waters (all ships have a right to be there), but where Russia control the natural resources (Fish for example). Russia claims the boat was fishing Russian fish, which is a bit ridiculous given the small time the Lithuanian boat spent in the Russian EEZ.
The ship was boarded and the crew sent to Russia by helicopter after refusing to go to Murmansk. It should be noted that this happended outside Russia's EEZ, where they have no juridiction whatsoever.
As for the Estonian intelligence agent, Russia claims he was in Russia, Estonia (somewhat more convincingly) that he was in Estonia. Estonian border guards and their Russian counterpart noticed the fighting on the Estonian side of the border, near a border crossing: Russian special forces used radio-jamming equipment and smoke bombs to capture the Estonian guy.
Also, if NK seized a US ship it wouldn't mean that they would be ready to invade. But a) NK hasn't invaded two of its neighbours over the last 6 years. b) NK isn't a huge country bordering the tiny USA, with historical control over the US and a significant Korean minority there which it vowed to protect. c) Russia isn't going to invade anyway, they'll again use salami tactics, to see what they can get with doing. We won't see the Russian army parading on the streets of Vilnius, but "little green men"? Why not?