I guess the lack of a decent computer system may be the answer, along with 3 different police agencies dealing with specific types of crime.
The Portuguese had no DNA database at the time iirc & no Sex Offenders Register.
Thinking back to how easily Ian Huntley managed to elude detection on what was supposed to be UK state of the art CRB system, I can quite understand why the PJ had limited knowledge of localise petty crime & crimes against holidaymakers who were unlikely to pursue matters.
The holidaymakers would only disturb the police to get a crime number for the insurance companies and would have had little opportunity to make much of a fuss anyway as a traditional time for them to be targeted was just before their departure date.
I'm not sure if any thought was given by the PJ to the possibility of Madeleine's case resulting from a botched burglary. As we know, her parents fell under suspicion immediately according to Mr Amaral. We don't know how the different forces rubbed along as far as an exchange of information is concerned ... but we do know that the PJ were in possession of DNA from one of the home invasions in which a child had been assaulted.
So there must have been an element of involvement there because of the serious nature of the offence. The British ambassador also knew about the assaults ... therefore the PJ must have known about them.