I think missing money is the least of your worries. How do you know your son didn;t find it? It is your word against theirs, you are never going to win.
And yes, they can search without you present:
Search of premises on arrest
PACE provides the police with clear authority to enter and search premises after an arrest. If you have been arrested for an arrestable offence, the police may search premises occupied or controlled by you for evidence of that offence or of some other arrestable offence connected with or similar to that offence. The police do not, however, have power to enter and search after executing an arrest warrant in extradition proceedings. The police officer conducting this search should normally have with him or her written authorisation on the Notice of Powers and Rights for the search by an officer of at least the rank of inspector.
If you have been arrested for any offence, not just an arrestable offence, the police may enter and search any premises you were in at the time of the arrest or immediately before it for evidence of the offence for which you were arrested. Again, in both cases the police are only permitted to search to the extent reasonably required to find the evidence sought and if the search is excessive, you may have the remedy of a police complaint or a civil action against the police.