I can confirm that the latest image didn't have any issues installing 
kernel headers...

hemant@beaglebone:~$ sudo apt-get install linux-headers-`uname -r`
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
0 upgraded, 1 newly installed, 0 to remove and 26 not upgraded.
Need to get 10.8 MB of archives.
After this operation, 75.0 MB of additional disk space will be used.
Get:1 http://repos.rcn-ee.com/debian stretch/main armhf 
linux-headers-4.9.78-ti-r94 armhf 1stretch [10.8 MB]
Fetched 10.8 MB in 4s (2,623 kB/s)                      
Selecting previously unselected package linux-headers-4.9.78-ti-r94.
(Reading database ... 34488 files and directories currently installed.)
Preparing to unpack .../linux-headers-4.9.78-ti-r94_1stretch_armhf.deb ...
Unpacking linux-headers-4.9.78-ti-r94 (1stretch) ...
Setting up linux-headers-4.9.78-ti-r94 (1stretch) ...


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