Is there any filter or action hook to remove layout classes from appearing in my templates?

You may use the following code (either in your active theme’s functions.php file or in a custom plugin):

// This line is preferably be added to your theme's functions.php file
// with other add_theme_support() function calls.
add_theme_support( 'disable-layout-styles' );

// These two lines will probably not be necessary eventually
remove_filter( 'render_block', 'wp_render_layout_support_flag', 10, 2 );
remove_filter( 'render_block', 'gutenberg_render_layout_support_flag', 10, 2 );

The above code should remove the classes like is-layout-flex, is-layout-flow etc.

Caution: These are added for good reasons. So, unless you absolutely have to remove these, I’d suggest you to go through the following links before making the final decision: