To my understanding, yes, that will be an issue. A data class can be populated by asset or by custom inventories. In other words, unless my brain is not awake yet, without asset, the only supported method of updating custom data classes is using a custom inventory.
I'd try inserting data using SQL to see if that changes the behavior as you suggested in your first post. I'd be interested to hear if that solves it. I know custom data classes do not always behave identically to existing data classes (for example, they do not appear in the report builder), but it seems that's not the case, since other custom data classes appear, provided they have data.