I was wondering how efficient using prepared statements in the mapping file vs prepared statements in code?

We have an application that has roughly 200+ prepared statements and it takes a while to load, up to 50 seconds or so but when I removed those statements the app loaded up much quicker....probably 20 seconds or so. So its seems like an obvious that the prepared statements caused longer load times.
So my question is how does this affect runtime and application resources? Are the longer deployment times a trade-off for better DB query and application performance? I ask because we are potentially in an environment where we would need to deploy multiple instances of this app on a single server and I'm trying to figure out how badly all these XML prepared statements are going to hurt server resources and possibly not less us deploy as many as we would like.