Ektron's metadata isn't intended for large chunks of data / content. So, yes, you will find limits there.
Here are two things you might try as workarounds.
Most direct:
Use the Ektron Library. Go to the Library tab and click on the Root node and view Properties. Add an extension to allow you to upload your JSON-LD as a file. Use metadata on the content item to reference the uploaded file. Combine the two upon output.
If you want the JSON-LD to be editable within the CMS...
Gaming the platform a bit
Create a new SmartForm definition and include in it a single plain-text, multi-line field (not Rich text). This should hold your JSON-LD. Set up a folder and, if your version supports it (you didn't specify CMS version, so I will assume relatively recent), set the folder to be non-searchable so these things don't come up in site search results. Add a restriction to the folder to only allow the Smart Form definition you just created. Create your JSON-LD there using the plain-text field. You should be able to store up to 1MB.
Same as above, add your JSON-LD as text then use a reference to this item from the content you want to use it.
The metadata in this case (and possibly the library one, though I'd have to test and I don't have an Ektron environment for development anymore) will give you the Content ID for the object holding your JSON-LD. You'll have to make another API call but will give you the solution you appear to want from above.