I want to make show/hide logic more maintainable in my codebase.

Because they are too faraway located in separate js files, it hard for people to maintain.

The flow in my codebase is:

require.js init (hide the target DOM at first) → app.js → load_comments.js (show the target DOM if the comments length > 0)

main.js (require.js manifest file)

$("#target_dom").hide();

app.js

define([
    'load_comments',
    "jquery"
],function( comments, $){

    return {
        initialize: function(){
            console.log("app.js initialized");
        }
    }
})

load_comments.js

var CommentView = Backbone.View.extend({
    el: $("#comments_section"),
    render: function() {
        var notNullComments = comments.wellFormedComments();
        if (notNullComments.length > 0) {
            $("#target_dom").show();
        }
        var html = commentsTmpl(notNullComments.toJSON());
        $(this.el).append(html);
    },
});

From a once over:

• load_comments should follow lowerCamelCase -> loadComments
• Avoid console.log, at least wrap it in something that also takes in to account message severity and filters on that message severity
• Personally I would have used either comments or wellFormedComments instead of notNullComments
• It seems that if there are no comments, that you should get out, and not do the JSON parsing and the html appending
• Where is commentsTmpl defined? Smells like a global variable
• It is very confusing to have #target_dom there, I am guessing that it is a subelement of #comments_section, but I would have called it #comments probably?
• Even more confusing is that you append the html to #comments_section and not #target_dom

All in all, I would go with something like this:

var CommentView = Backbone.View.extend({
    el: $("#comments_section"),
    render: function() {
        var comments= comments.wellFormedComments();
        if (!comments.length) {
            return
        }
        $("#a_descriptive_id").show();
        var html = commentsTmpl(notNullComments.toJSON());
        $(this.el).append(html);
    },
});