How can I rename my files with datestamps in Aperture and keep them in order?
The solution is to avoid direct import by Aperture.  Import them onto the disk using your camera software, or by using a card reader, or if you camera is suppored as a 'device' then direct copy in Finder.

Run the command:

exiftool  -d %Y-%m-%d_%H-%M-%S '-filename&lt;${datetimeoriginal}.${subsectimeoriginal}.%e'


This will format the filename as 

2016-12-09_20-27-21.20.JPG  
2016-12-25_14-29-00.70.NEF


Exiftool can be downloaded from here: 

http://owl.phy.queensu.ca/~phil/exiftool/

Note that the subsecond time can be either a 2 or 3 digit number -- either centiseconds or milliseconds. My d7100 reports 2 digits, but the last one is always zero.  So internally it's using a decisecond timer.