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: linux-headers-4.9.78-ti-r94 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) ... Thanks... -- For more options, visit http://beagleboard.org/discuss --- You received this message because you are subscribed to the Google Groups "BeagleBoard" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/beagleboard/1e86f69d-6026-4ffd-98f9-ffe92559789a%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
