I think there are two main reasons why Nintendo is so aggressive about their IPs.

1. Concerns over missing out on future revenue. Nintendo doesn't have anything close to a complete back catalog in their Virtual Console, nor do they consistently offer other good options to purchase old games. However, they want to leave the door open to offering that in the future. Emulation, in their view, "robs" them of that possibility. They feel that since they own these games, they should have control over which ones are made available and how, and the only option for fans to get them should be to go through them. If emulators are easy to find on a platform like Steam, people new to gaming might assume the emulators are endorsed by Nintendo, which irks them because they don't get any sales revenue from that. If they bring Nintendo games to Steam-- and that's a huge if-- they want Valve to pay through the nose for them.

2. Protecting the integrity of their original characters. Pokémon is the example I'm most familiar with, so I'll go with that one: Nintendo is uncomfortable with fan games and even the "Nuzlocke" fan challenge, where Pokémon are described as dying in battle instead of fainting. They want Pokémon to be seen as a family-friendly, all-ages franchise, and rom hacks take away that creative control. Additionally, Nintendo has no control over what kinds of websites host roms for download, and they certainly don't want most of these websites to be associated with their brand. Like with emulators on Steam, people unfamiliar with this issue might assume Nintendo tacitly endorses distribution of all sorts of roms that don't have that classic Nintendo seal of approval.