Yes, it's become A Thing. Yes, it actually happens from time to time. Is it unavoidable or unstoppable? No, but you do have to be aware of how to overcome it, which is usually by beating the Corp's traces, trashing the key cards for the combo, forcing the corp to burn a Jackson (or just trashing him when you see him), or throwing down double or triple plascrete... Probably the thing that fights this combo more than anything else is not allowing a Jackson Howard to stay on the table for any length of time.
As for your suggestion, I agree with you and I personally think that the card should have had a final caveat: "The value of X cannot exceed the most expensive program or piece of hardware the Runner currently has installed." FFG is doing a great job with the game so far, and Power Shutdown is one of the first cards I've seen them print that is badly-designed or thought-out. I think the intention of the card is to give corp players a way to remove pesky, low-cost programs and hardware such as Datasuckers, Faeries and Clone Chips, while keeping expensive Runner programs and consoles like Femme Fatale, Torch, and Toolbox relatively safe.
Having played Warhammer 40,000 and several other "I go, You go" games where player interaction is reduced or nonexistent during turns, I've come to dislike anything that minimizes player interaction. This includes Power Shutdown, Cerebral Imaging "7 points in one turn", as well as NBN TWIY rush decks.