Here's a collection of some of the most commonly asked questions (and answers).
If you're called to testify or otherwise appear in court, you will be asked to take an oath. Standard procedure is that you will be asked to affirm the oath recited by the magistrate, then kiss the crucifix. This is not a requirement. If you tell the magistrate or official that you are not religious you will be instead asked to "solemnly declare" (tiddikjara solennement). In all but the words and ritual, this is identical to a religious oath.
This applies in any and every situation in which a person can be required to take an oath, including taking an oath of office etc.
I don't think this issue has been tackled officially yet, but considering that the constitution declares Malta's religion to be the Catholic one, and that religion is part of "mandatory education", I think they can make the case for teacher-led prayer easily. On the other hand, no student may be forced to participate due to freedom of religion.