The list was on a hard drive on a laptop. If the laptop was online and if Silva knew where he had to look for, yes, he could have hacked on to the laptop. But considering the sensitive information of the list, it's plausible that this was kept offline, which means he would have no way of being able to hack into the laptop. Even if the laptop was online, Silva would have to know
- the specific information of the laptop
- when the laptop would be online
- having to break through any firewalls that might have been there.
As for how he could hack into MI6, he was an operative for them for many years. It's also possible that when he wasn't going on missions for MI6, he got the information necessary to know how to get into their system. I mean, James Bond was able to log on to M's computer in Casino Royale, so there must be some kind of weakness MI6 has yet to fix. And the MI6 servers were always online, and always in the same location, so that made getting past the firewalls the only major obstacle for him.