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This has nothing to do with mining, nor security. If you run a masternode, you are supposed to be providing a service, but as you explained for at least the first year of masternodes and continuing for an indefinite period going forward, the cost to provide the service has been negligible, reducing it to a redistribution scheme funneling coins to people with masternodes (and some have hundreds of nodes -- not surprising since as you say the cost to operate them is so low).
To avoid being a redistribution scheme, a masternode system would have the node earnings (at least most of the earnings; a small subsidy might be justified) coming from fees paid by people who actually use the service.
The aim is to have zero fees for normal use, there'd be fees for large numbers of transactions but regular users should never have to pay to use the network. Hard to see how that'll scale as coin output is reduced but everything is being done step by step, the governance system has had time to get established now and is getting an update based on how it's worked so far and it'll be the same for the fee system, test it, tweak it, etc, etc.
Same with the masternodes, the rewards have been big so far but they'll start dropping now that's established, it has to stay profitable to run the second tier but they could come down a lot and still give a very good return. Ultimately that could lead to centralisation, need for dedicated hardware rather than just renting a VPS at the going rate but if things look like they're going that way it'll be addressed.