First it is important to state whether a thesis is published or not. In some countries theses are formaly published under an ISSN and ISBN number, in others it is a pile of printed paper that is seen by a very few. I am sure anything between these etxremes exist as well.
If you have a published paper and need to put it into your thesis, either as a reproduction of the printed version (the pdf from the jorunal) or you reset the final revised manuscript, you defintely must get permission from whoever holds the copyright. This could be author and publisher or publisher only, it varies between journals. The reason why the copyright applies also to re-typeset manuscripts is because the copyright covers any corrections the copyright holder has made to the manuscript.
In reality, I doubt many publishers care, but on the other hand it never hurts to get the permission in writing. since a thesis is usually published in very few copies, it usually is not a problem. But, if the thesis is also freely available as a pdf it may again be questionable and a too obvious infringement on copyrights.
The second part is quite tricky, is it a duplication to publish both in a thesis and a journal. If the thesis is an official publication, then yes it would be a duplication per definition. I know some journals are very strict about these things. To be more pragmatic, I wold say that it depends on how the thesis is distributed. If it is printed in a very small number and not freely available as a pdf then publishing in a journal should be possible. But I am sure this can be controversial and no consensus exists as to what is a reasonable middle way. In my field, manuscriprs are published in a thesis with ISBN and ISSN numbers (printed in about 200-3000 copies) but not available as pdf. These manuscripts are then later improved and sent off to journals. I think journals in general tend to turn a blind eye to the cases where thesis materials are recirculated.