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I don't know of any "dummy" call you could make to DynamoDB that would prove that the database is in any particular state. Calling the control plane to (say) describe a table isn't going to mean that data can be retrieved or stored in the table.
If it were me, I'd make a GetItem call at a period less than the Route53 health check timeout (or, as you say - when the health check comes in). Not that even this isn't a 100% test but it should be "good enough". And it isn't a guarantee that the next call won't fail - because things fail all the time (great quote from Werner Vogels).
Tracking the last call status is pretty good but you've also pointed out the problem there.
Yes, extra calls and cost to get an up-to-date status. Really depends on whether that is worth it for you.
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Agreed, the cost of a half RCU for each health check is cheap. How many health checks do you get for a dollar? If using provisioned capacity, about 50 million calls, by my math. Health check every 5 seconds? That dollar buys you 8 years of health checks.
Regarding the cost, my calculation (after I posted the question) was
In my experience with AWS pricing, everything is always "ridiculously cheap" or "ridiculously expensive". Calculations like this just need to make sure they aren't wrong by a factor of a thousand or a million, due to e.g. confusing per-second and per-month prices!