So the thing about appropriations is - they actually have to spend them unless it says something else.
It's not like a budget. It's an order to spend money a certain way. That's why generally congress is said to have the power of the purse - they give the directions on how money is spent.
So appropriations come with directions, time frames, etc.
The executive branch must spend them as directed, and they must be applied to the specific purpose as directed.
This is also why you will sometimes find federal agencies or the military spending infinite money towards the end of the fiscal year, because they are just making sure they spent all the money they were supposed to. Again, sometimes the appropriation says "spend up to", etc. But whatever it says, they have to do it.
So if they say "you have to spend 1 billion on USAID", they must in fact, spend 1 billion on USAID.
Let's take the agencies that are specifically authorized or created by congress out of the picture - they literally can't disband these (and i don't believe they've tried yet). These are usually the things created or later authorized by bills that say something like "their shall be an office of the xyz" or something similar.
So for example, CPFB is here: https://uscode.house.gov/view.xhtml?req=(title:12%20section:...
(I just picked a random one, the establishment language is fairly standard, the rest i have no opinion on :P)
Given it is created and provided for by law, it must be disbanded in the same manner - legislation that removes it.
So if we are sticking to the other ones - it basically comes down to whether an appropriations bill allows it in some fashion.
Does it say "1 billion must be spent on USAID" or does it say "1 billion must be spent on giving aid to ukraine" or does it say ....
That is what in practice, enables or prevents an EO from disbanding an agency that is not specifically provided for by congress.
At least, as far as money/etc goes. There may be other reasons they can or can't disband an agency.
For example, Congress has a congressional research service that provides it with information. It is basic to the functioning of congress (or just slightly above basic). Whether established by law or not, it's unlikely to be constitutional for the executive to disband an agency that another branch depends on, since they are supposed to be coequal branches. This has rarely, if ever, been tested in practice though.
Even when different branches have hated each other with a passion in the past, the degree to which they would test the limits of constitutional power while pissing on each other was fairly restrained.
There are a few exceptions, but they are definitely the exception and not the rule.
Also keep in mind - while the president has some special powers, the general purpose of the executive branch is simple - to faithfully execute the laws. The only discretion in even doing that comes from the laws themselves and the constitution's description of the executive's discretion.
EO's (no matter who makes them) were not intended to be a path for the executive to do whatever it wants, and use power not granted to the executive
I say this not offering a view on the legality or not or wisdom or not, just trying to make sure i answer your question completely.