Disabling creation of unnecessary files on my external hard-drive?
Those files are created on other external drives as well.

The files that start with ._ are AppleDouble files that are used to store metadata like extended attributes and ACLs on unsupported filesystems. If the volume doesn't support the native formats, the AppleDouble files might get recreated even if you delete them. If the volume supports the native formats, the AppleDouble files are ignored, and you can either delete or merge them:

rm /Volumes/Volume/._*
dot_clean -f /Volumes/Volume # flat merge (default is recursive)


It's usually safe to delete the ._ files in any case. The .Trashes folder on my USB drive only had a com.apple.FinderInfo extended attribute:

$ sudo xattr -l /Volumes/WD/.Trashes
com.apple.FinderInfo:
00000000  00 00 00 00 00 00 00 00 40 00 00 00 00 00 00 00  |........@.......|
00000010  00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  |................|


.com.apple.timemachine.donotpresent* files are not created if you enable this setting:

defaults write com.apple.TimeMachine DoNotOfferNewDisksForBackup -bool true


Spotlight can be disabled with mdutil -i off:

mdutil -i off /Volumes/Volume
rm -rf /Volumes/Volume/.Spotlight-V100


Deleting .DS_Store files:

find /Volumes/Volume -name .DS_Store -delete


This makes deleting files on the volume in Finder delete them immediately:

sudo rm -r /Volumes/Volume/.Trashes; touch /Volumes/Volume/.Trashes


BlueHarvest can remove most of those files automatically: