From my experience of playing against Skorpios, I haven't found lockout scenarios very common. Issues I tend to run into are:
1) Fear of running, due to not having Saccon or strike out, thus allowing the corp to get away with an otherwise unsafe score.
2) Not being able to steal an early agenda due to not having right breakers (basically a standard problem against rush).
3) Losing a breaker, and having to fallback on my less efficient AI instead.
All of that seems to fall into the realm of the corp just having a different way of creating scoring windows. Some decks do it with upgrades and taxing ice, some do it with tag tax, some with the threat of death. Skorpios does it by disrupting your boardstate. If you play carefully as the runner, getting locked out is usually avoidable.
I've lost one game to lockout, where a Skorp player advanced an underway renovation, trashed Refractor off the top, and removed it from the game. Later they found Hortums and triple advanced them, preventing Dai V from breaking them, and I couldn't get in anymore. That type of thing I would see as NPE. But that doesn't seem to be the way most Skorpios decks are playing.