Yes, in varying degrees. In the US, Malcolm was mostly rated PG, for parental guidance suggested. A number of episodes were rated TV-14 for 14 and over, but they are often censored (with scenes cut) by channels and then shown as PG.
In the UK the series was restricted to 12 years and over, due to moderate sex references.
Germany applied the yellow FSK label of 6 years and over, while in France the show was 'tous publics' - suitable for all.
In Australia, it was labelled PG due to mild sexual references and infrequent coarse language, which means parental guidance under 15 is recommended, though not obligatory.
In the Netherlands, it is rated 6 years and over as in Germany, with additional labels warning against some violence, terror and coarse language.
As for another type, pre-production censorship, in the script for "Water Park", at the end of Season 1, the babysitter (Bea Arthur) was supposed to kidnap Dewey. Producer Fox vetoed the idea, because it could imply condoning child abduction. Also, shots in the series of Hal running naked, and bare buttocks were often covered by pixel blocks. Other examples are that Fox would only allow smoking scenes if it was implied it was an addiction and harmful, and the bleeping or modification of curses, like jeezle for Jesus by Hal in the "Red Dress" episode.