Which method has better performance
This is essentially impossible to answer.  You have one part of your question, wrong


Your first method uses a single node_load_multiple() with multiple node_save
Your second answer uses multiple node_load() with multiple Entity API calls


My gut tells me the first will be quicker, as a single node_load_multiple() is typically more performant than multiple node_load() calls, given the same set of nodes.  You also aren't creating the the metadata wrapper objects.

However, you need to do the benchmarking on your system.  There may be a difference, but it may be small enough to not make a real imapact.  Some things that make cross-system benchmarks unreliable


entitycache can have a tremendous impact on a system, especially if you use a non-SQL backend for it
the number of fields on your node can effect how long the wrapper creation process takes, and also how long the node_save() takes
APC and/or OpCache usage and configuration
PHP version
MySQL configuration (or whatever database backend you are using), including some of the Drupal-specific tricks that can improve performance
The number of hook_node_update() instances that fire for each save