Problems might occur, indeed. At least according to Murphy.
NTFS is a journalising (it keeps a log) file-system. If the log and it's current state doesn't match upon reboot the filesystem perform a check and undo any failed changes, thus bringing the filesystem back to last consistent state. This goes pretty fast and there is no need to check the whole MFT/partition/drive.
The second question beets me. Why should that be bad? I have always mixed different filesystems according to my needs. If you plan carefully there are no drawbacks. To avoid unpleasent surprises you have to do some thinking though. Not all os's accept filesystems placed by random, or you might get unpractical drive letters.
All my computers (well, in the house - used by my family) have their C:\ formatted in FAT16. Then there is a mix of different partitions formatted in FAT32, NTFS and ext2fs, swap-formats and also other temporary stuff. The main computer have three harddrives, a total of 12 partitions formatted in four different formats (for the moment).
Feel free to ask about opinions in this question - I'm sure you will get some different ideeas and opinions in return....
