How were Kate's worst fears confirmed, then? You say the shutters, doors, etc. were not enough to indicate abduction. What additional evidence was found?
Well as has been said, straight away she assumed that Madeleine had been taken, this I suggest is her worst fear as it would be for any parent.
At that time the shutters, door etc. were not indicative, but let's be clear we are talking within a specific timeframe. The only thing that would be indicative at this precise time would be a witness seen making their way away from the apartment with a child that was Madeleine. I think under those circumstances, at that precise time, Kate would be well founded in believing that Madeleine had been abducted.
As such, there is no evidence indicating what happened to Madeleine, hence why the investigation is somewhat at a standstill. The Scotland Yard enquiry runs out at the end of this month so it will be interesting to see what, if any conclusions they are able to publish.