That means 99.9% of your coins are cold staking, and 0.1% are hot staking. If you close your wallet, all your coins except 0.1% would continue staking. 

Cold Staking Activation is a process which measures the # of your outputs which have converted to the new cold staking smart contract. A 99.9% activation implies that 99.9% of your coins are "NOW" cold staking with 0.1% still waiting to convert (so make sure that staking node is online!!). That is how much of your coins are "eligable" to receive staking rewards. So you aren't losing staking entirely by not being at 100%.

To push it to 100%  you can try Zap tools from this guide