As most of the folks here have already mentioned, a humidity level of 46% is more than acceptable, so you really can ease your concern about that.
Regarding the whys and wherefores of your 46% reading ... well, the people both here and at Ameritage gave you your answer: your case is designed to breathe, so the humidity will not continue to just rise and rise. And, I suspect, that the humidifier and case have some sort of property whereby the internal humidity gets stabilized at a level (in this case, 46%), and is simply maintained, regardless of the outside humidity. And, if the outside humidity increases or decreases significantly, the effect would be less on the internal case humidity, and more on the rate at which your humidifier releases moisture and how frequently you need to add water to it.
But the takeaway message really ought to be that you can kick back, spark open a cold one, and relax in the knowledge that your uke is quite comfy. There is no need to obsess over reaching 50% humidity, particularly if your case can maintain 46% on a consistent basis.