Different header for different page templates

https://codex.www.ads-software.com/Function_Reference/is_page_template

example:

<?php if( !is_page_template('popup.php') ) : ?>
NAV MENU CODE HERE
<?php endif; ?>

thank you!

sorry quick follow up, is there a similar fix for CSS?

For example, on my main pages I have:

#site-title {
	text-align: right;

but on my popup.php I’d like this:

#site-title {
	text-align: left;

your theme uses the body_class() function in the body tag which outputs template specific css classes;
https://codex.www.ads-software.com/Function_Reference/body_class

you can use these to style elements dependant on the page template;
example:

.page-template-popup-php #site-title { text-align: left; }