No problem at all.
Portugal is in the EU and EU law requires all member states to admit anyone who can prove that they're a citizen of any member state, by producing a valid passport or national ID card, right up until the expiry date of that document.
In general, the only countries which specify a certain period of validity on your passport are those which require visitors to leave within a certain period. Since you and your children (as EU citizens) have the right to live and work in Portugal, you can never be required to leave the country, so it would be impossible to specify a certain period of passport validity.
Chris