Here's a short configure.ac example with an autoconf test to check whether the linker supports version scripts.
I spent a few minutes searching for such a check and no results popped up, so I resorted to writing my own.
The code below might be useful for others looking for such a code snippet, and can be easily adapted to suit specific needs.
AC_INIT(--version-script test example, 0.1, matteo.vescovi@yahoo.co.uk)
AC_PROG_CC
AC_PROG_CPP
AC_MSG_CHECKING([whether linker supports version scripts])
cat > conftest.map <<EOF
VERSION_1 {
global:
main;