According to him, the named queries are not only parsed at startup but they also are executed which would slow significantly the startup.
No, this is not true. Named queries are not executed at startup. They are being parsed and compiled at startup time, but not executed against a database.
Is it right and if so, is there any configuration to prevent hibernate
from executing the queries?
If you are asking about how to prevent compilation of such queries, AFAIK there is no way to disable it.
Although I agree that huge amount of named queries can slow down the application startup, but typically it is not a significant factor.
You have to choose between startup and runtime performance. Personally I usually make some of my JPA queries a named queries (the ones, which runtime performance is essential).