Disallow /node/ in robots.txt
Having you pages accesible both via /node/* and /somealias leads to duplicate content and should be avoided as this can cause an SEO penalty. Under normal circumstances you could take a look at the global redirect module


  GlobalRedirect is a simple module which…
  
  Checks the current URL for an alias and does a 301 redirect to it if
  it is not being used. ...


It saves you from alteting robots and comes with some additional benefits.

Related to your question:

Since they are different paths, blocking one does not affect the other. And as explained above it is advised to prevent crawlers from indexing both. It should be safe to block one of them.

However, for Google indexing your /node paths, they might be in use somewhere. So first check your existing links and make sure there is nothing linking to those paths. Then add it to robots. (If it is still in use when you block it, you risk certain parts of your site not getting indexed.)