*Keyboard is messed up, apologies for horrendous grammar*
If you dont like long planning, simply dont allow it regularly. Design runs that dont require extensive planning, or make the information gathering process difficult, and time consuming. Mr. Johnson does not like to be kept waiting, there are deadlines to meet.
As the GM, you make the rules. Im not advising you to be cruel to your players, but there is nothing wrong with taking full advantage of the tools at your disposal. An example of this would be to line up a run that they would normally plan for hours, but have them get jumped during the planning process. To make matters worse, during the fight one of the villains snatches someones commlink and escapes, only have to have everything go completely to hell. Turns out that commlink is most likely in the safe at the Yakuza boss headquarters and he is the very guy you were supposed to take out. Now you need to do it swiftly, and before they have time to access sensitive data on the commlink(sure you can be careful, but everyone can slip up from time to time).
That is just one of many examples of a run that you can catch a breather on and deny them the chance to spend 3 hours planning things out.
Another possibility is to make better use of knowledge skills, and instead of rolling out too many tasks, you could make a small number of rolls and tell them what they find out. You dont need to kill a lot of game time hammering out every single detail, if they need more info, its okay to make it easy or at least fast, once in a while.
I like to GM at a somewhat quick pace, while I give plenty of time for roleplaying bar scenes and meets etc, I also dont want to sit around planning for half of my game session. You need to find ways to make that process quicker, and you definitely cant let them deliberate for hours. 30 minutes should be the absolute maximum. The players have contacts, knowledge skills, active skills etc, you can simply hand out a bit of info if things are taking too long, anything it takes to keep the game entertaining for you, and that information doesnt even need to be accurate.
Also, I would highly suggest not letting their master plan make for a boring run. You should definitely keep them on their toes, its rare that any plan goes perfectly. People make mistakes, bad things happen, you gotta keep it interesting.
Tired rant coming to a close, but essentially, find ways to move the game along at a pace that everyone is happy with. Once you GM with that concept in mind, youll find your sweet spot and you and your players will have a lot more fun.