Hi Guido,
1) Those areas should be tagged with a NODATA value. If they aren't already then you should be able to set that with a RasterBandNodataSetter transformer. Then it's up to your viewing software to recognize them as NODATA and display them transparently.
2) You can create a TAB file for jp2, but not a prj. So, what you can do is use the CoordinateSystemExtractor to extract the coordinate system, then use that in a CoordinateSystemDescriptionConverter transformer to convert it to Esri WKT. Then I think you just need to write it out to a prj file (say with the AttributeFileWriter)
Hope this helps
Mark
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Just curious Mark, does that work (Question 1)? I thought .jp2 was lossy compression, so in fact the balck areas aren't in fact "black (RGB of 0,0,0) but in fact close to it? So therefore you cannot set it to NODATA.
I've had the same problem with any lossy compression (ECW, SID, JPG).