It depends on how they are used.
checkNotSaved = true/false is NOT an issue in 1.9
Becuase it is used like in code below The variable itself is NOT
written out in javascript. This is a good solution cause uneeded
javascript won't be sent to the client at all.
However if the config value is needed in js-code it should be sortof
escaped to text. There is probably something in smarty that could do
this (or just add a function booleanToJavascript() )
{if $tlCfg->gui->checkNotSaved}
<script type="text/javascript">
var unload_msg = "{$labels.warning_unsaved}";
var tc_editor = "{$tlCfg->gui->text_editor.all.type}";
</script>
<script src="gui/javascript/checkmodified.js" type="text/javascript"></script>
{/if}
Regards,
Eloff