I'm parking the car (gen. 2) a long while, so I checked the manual which shows the deactivation button on/off positions. It show the button sticking out more = the off position. However, the car symbol still blinks on the dashboard.
I assume that is the SKS button that you refer to, that turns off the SKS system. The blinky light will still be there, as it is a function of the vehicle immobilizer which is always active. The light will go off when you insert the key fob into the dash, as in a non-SKS type car. It's current consumption is minimal. If you leave the car for a long period, you will want to be sure of the quality and charge of your 12V battery to insure a reliable start.
What does "long while" mean? If more than a month, you should first charge up the 12V battery using a battery charger - then disconnect the negative cable where it attaches to the body.