I once left my Jazz for 7 weeks, and it started without problems when I got back to it. But the battery was a lot younger then. Does your stop-start work? If not, and you get the low battery warning, that's an indication that your battery is aging and leaving it for an extended period might be a risk. You might consider a solar charger to compensate for the parasitic drain on the battery.
If you do decide to disconnect, there shouldn't be any lasting effect, but you'll need to ensure the car's in a safe location (obviously the alarm won't work) and know how to open it without power. You may lose settings in the infotainment system as well.
