Need to render 1100 masternodes unreachable? No problem - SNMP amplification attacks will let you use a handful of boxes to amplify the bandwidth under your control. When a datacenter sees a clear flood of traffic for a particular IP address at the datacenter their response is always automatic and the same - their upstream data provider blackholes that IP address at the upstream bordergate.
This is actually a far better problem for an anonymity coin to have than a protocol weakness.
The criticism above is fair enough as far as network serviceability goes, but if it doesn't have any impact on the anonymity of historical transactions in the blockchain and they remain safe, then the job is more or less done.
All networks are subject to DOS attacks, whatever their nature. It's not a significant criticism of an anon-coin to say that it may be exposed to DOS attacks - who cares as long as the blockchain's safe ? Websites get DOS'd, eMail gets DOS'd, everything gets DOS'd. You just mitigate it, setup nodes elsewhere and carry on. The technology and the whole approach evolve to become progressively more optimal and resistant to serviceability attacks.
On the other hand, networks that rely on purely protocol based anonymisation are a ticking time bomb because if a crack emerges then you've got a potential can opener for the whole blockchain's worth of historical data.
That's why I think Darkcoin's got the right approach. If I want to make an anonymous transaction today, I don't give a sh*t about whether it can be DOS attacked tomorrow. But I DO care about my historical transaction staying anonymous.
The other blatant flaw in the "it's vulnerable to DOS attacks" critiscism is that it assumes a static network. The masternode network is not static, it's constantly moving. A masternode can be setup and hosted in minutes and then moved in minutes if need be. It's a moving target "cloud" that is not stuck behind a fixed DOS'able firewall in the way fluffypony alludes to.
So all in all, I think this post, far from exposing any weaknesses, only goes to demonstrate its fundemantal strength of approach in offering massive redundancy and pre-emptive anonymisation using the 2-tier system.