Large scale botnets have little incentive to mine a new cryptocurrency and probably won't prevail for a while. While it is a possibility in the future, healthy amounts of legitimate miners will weaken their effect.
On the flip side, while botnets can suppress Neptunium's value and distribution, they help support and strengthen the network by mining. Viable botnets can exist for any ASIC resistant coins. Although we see botnets do mine other CryptoNight coins like Monero, it doesn't stop them from being successful.
Botnets are undesirable, and small scale botnets may appear in the future. However, I don't see Neptunium going through any botnet epidemics nor having a fatal effect on our coin. I obviously can't say for sure what will and won't happen, but that's my thoughts on it.