[...] in many cases there's already an error handling system in place to deal with this condition.

Could you elaborate on this? Do you mean that many plugin and theme developers expect their update server to return valid JSON that is missing certain entries, and they've designed their code to handle that case? This seems unlikely to me.

I worked on at least two projects where the call to the update endpoint returns a JSON without that information, because it's used for premium products. If a valid licence is not found, the JSON is valid, but it doesn't contain any plugin meta. That's different from the update server example, which always return the plugin meta, but removes the download URL.

In other words, the call to "get latest version" may return a response that is valid in such context, but doesn't contain the expected meta. That condition is handled gracefully, therefore there is no need to raise a notice in that case.

In addition to that, both the client and the server plugins I worked on use their own logging system, instead of relying on the trigger_error() function. That makes the notice redundant, as the logging has already been performed.

If the server response doesn't contain any plugin meta, it doesn't seem like a valid update API response even if it contains syntactically valid JSON. Could you perhaps make it return an error instead, like a 403 Forbidden error to indicate that the license is not valid? The response body can still contain JSON if you need to pass some information to the plugin.

The update checker already contains some code to handle non-200 responses and that seems like a better place to deal with this issue than the metadata class.

In this specific case, that might not be that easy. An "invalid licence" is returned with a response code of 200, because it's considered a successful request. It all works fine, the only issue is that PHP notice, which is unnecessary to anyone except the developers. In any case, I will propose the change on the response header, maybe it will work too.

In general, the PHP notice is useful for debugging, and it's only shown when the WP_DEBUG constant is set. The issue is that such constant is often enabled in production, so we can't rely upon it being disabled. That's why I have a separate "debug mode" for each component I develop. It allows to enable that mode only for the ones being tested, without polluting the PHP log with unexpected errors.

I wouldn't be opposed to the idea of adding a "debug mode" filter. The update checker already has something similar in the form of the $debugMode property of the Puc_v4p9_UpdateChecker class. You can set it to false to override WP_DEBUG settings and disable some notices, but it currently doesn't affect metadata parsing.

Still, I think this kind of thing should happen in the update checker class, not in the metadata parser. Maybe the parser could call the triggerError method on the PUC instance instead of directly triggering a notice...