Restoring this for posterity:
See Jim's answer This content in this answer would mean the scripts would not be marked as executable upon installation.
For supplementary scripts, you should use the inst/ folder. From the Installed files - Other languages section of Packages:
The convention is to put scripts of this nature into a subdirectory of inst/, inst/python, inst/perl, inst/ruby etc. If these scripts are essential to your package, make sure you also add the appropriate programming language to the SystemRequirements field in the DESCRIPTION. (This field is for human reading so don’t worry about exactly how you specify it.)
If you have other languages you want compiled, you can use a custom makefile. See the Compiling in subdirectories section in Writing R Extensions.