Before you say that DND Beyond won't let you homebrew classes, I already know that. But since you are able to change your stats to your will, you can at least simulate playing a homebrew class.

For example, say that you are simulating a homebrew class that has 1d6 hit dice, and you roll a 4 with them. You can then manually increase your max hit points by that and your constitution modifier if applicable. But what makes it more complicated are things like features. So that is my question: How can you simulate playing a homebrew class with DND Beyond?

Make a Race and turn it into a Class, that's the closest you will get. Because with a race it can be edited freely.

You can also use the item, spell, and feat system to create a facsimile of a homebrew class. It takes a fair bit of effort, but it is quite doable—I have a player presently who has hacked together the extremely complicated Unearthed Arcana Mystic class using Beyond. 

I would recommend choosing a “class” with the same hitdice as your homebrew class and create a subclass within that, with no additional bonuses (and possibly homebrew to negate your bonuses from the base class).  That ensures Beyomd tales your empty subclass level into account for things like proficiency bonus, HP, and the encounter builder

I think Lolths and Caerwyn give great answers, and are both right in that how you can emulate a homebrew class on DDB is going to vary from class to class.  Something like the Pugilist class that was really popular a while back would probably do real well as a subclass of fighter or barbarian ... something like the UA Mystic or various Witch classes floating around will likely need a combination of approaches.

So the productive question in the homebrew forums wouldn't be so much "How do I emulate hombrew classes" but rather "how do I emulate this particular class?"

That a cross your fingers that the future iteration of DDB will be more homebrew class open (I'd say it almost has to if it doesn't want to bleed users to platforms like the VTT competitors and maybe Demiplane where these things might be a lot easier).  

Important note: it is against the homebrew rules & guidelines to publish something that uses one game feature to represent another game feature (for example, using a magic item to mimic a persistent effect such as rage, or a race to mimic a base class). So while these suggestion are 100% okay for personal homebrew, please don't publish them

This is a really good idea. I do want to homebrew an Elementalist class with 1d6 hot dice. Sadly though, I'm not sure how you can remove class features with homebrew. Do you have any tips?

There isn't a way to remove class features.  There was talk of opening up the editor to allow homebrew "Optional Class Features" post Tasha's introduction of optional class features, but that was prior to the ownership change and doesn't seem to be on the drawing board anymore.  Really, the optional class feature editor would have been a de facto homebrew class generator, which may have something to do with the reluctance to introduce it to homebrew.