I modified my configure.ac to read:

AC_CHECK_PROG([ODBC_CONFIG], [odbc_config], [odbc_config], [no])

AS_IF([test "x$ODBC_CONFIG" != "xno"], [
    ODBC_CFLAGS=`$ODBC_CONFIG --cflags`
    ODBC_LIBS=`$ODBC_CONFIG --libs`
], [
    PKG_CHECK_MODULES([ODBC], [odbc])
])

ODBC_LIBS="$ODBC_LIBS -lodbcinst"

AC_SUBST(ODBC_CFLAGS)
AC_SUBST(ODBC_LIBS)

and then in Makefile.am I used:

libodbc_lib_la_CXXFLAGS = -I../../dbinterface \
    -DUNICODE \
    -DUNIXODBC \
    $(ODBC_CFLAGS) \
    @DBTOOLKIT@

libodbc_lib_la_LDFLAGS = -L../dbinterface \
    -ldbinterface \
    $(ODBC_LIBS)

I rebuilt everything but upon running the program I got an error that SQLInstallerErrorW can not be found.

However, when the Makefile just had:

libodbc_lib_la_CXXFLAGS = -I../../dbinterface \
    -DUNICODE \
    -DUNIXODBC \
    `pkg-config \
    odbc \
    --cflags`\
    @DBTOOLKIT@

libodbc_lib_la_LDFLAGS = -L../dbinterface \
    -ldbinterface \
    `pkg-config \
    odbc \
    --libs` \
    -lodbcinst

everything worked as expected.

But it is hard-coding the variables, which is wrong.