So "Do you want a book or magazine?" without the second indefinite article is wrong - how would you express that properly in Czech? [i.e. 'do you want something to read, I have both books and magazines?' as opposed to the given translation which suggests a situation in which I know you want something to read, but not which of the two types of reading material you want.]
They are not completely interchangeable. Only certain kinds of časopis can be called magazín and I would not use this word in this particular sentence.
the SSČ dictionary:
magazín, -u m
1. obrázkový časopis rozmanitého obsahu
2. informativní televizní pořad: zpravodajský magazín
obrázkový časopis is a magazine with many pictures