Based on the documentation, the reference to the actual field
Site__r.Account__r.Name looks the way to go but it is not clear-cut. (And with small numbers of records you probably won't see any difference.)
This is because (from Working with Very Large SOQL Queries):
primary keys (Id, Name and Owner fields), foreign keys (lookup or
master-detail relationship fields), audit dates (such as
LastModifiedDate), and custom fields marked as External ID or Unique
and (from Force.com SOQL Best Practices: Nulls and Formula Fields):
Force.com cannot index [formula] fields that: Reference other entities (i.e.,
fields accessible through lookup fields)
But there is this caveat (from Developing Selective Force.com Queries through the Query Resource Feedback Parameter Pilot):
Leading '%' wildcards are inefficient operators that also make filter
conditions unselective. As a best practice, use SOQL or remove the
leading '%'; although the Force.com query optimizer does consider
using an index even if you do use this leading wildcard, it will
choose to use that index based on the number of characters in the
search string and the number of matches that result. For these
reasons, it usually chooses to do a table scan. When you're querying
millions of records, the performance that a selective index gives you
can be significantly better.
An index allows a row to be found without the database having to search through every table row (a table scan) and can make a large difference to performance.
So it appears that by not using formula fields you open up the possibility that any pre-existing index is used and you can also request Salesforce support to add custom indexes and they will be used. But the wildcards you are using may cause those indexes to be ignored.
If you have an org with a representative amount of data in it, probably the best thing to do if this optimisation is important to you, is to create some unit tests and compare the results. As well as measuring the execution time you can get some basic information about the resulting query via the Developer Console Query Plan Tool (How To & FAQ).