Until Linq2NHibernate is ready for production, here is a method for keeping the specification logic encapsulated even if the domain code is different than the database query code.

Here is the specification interface, where I added the EnsureThatWillBeSatisfiedBy method:

public interface ISpecification<T>
{
  bool IsSatisfiedBy(T recipient);
  ICriteria EnsureThatWillBeSatisfiedBy(ICriteria criteria);
}

I am also using an extension for ICriteria:

public static class CriteriaExtension
{
  public static ICriteria EnsureItWillSatisfy<T>(this ICriteria criteria, ISpecification<T> specificationToSatisfy)
  {
    return specificationToSatisfy.EnsureThatWillBeSatisfiedBy(criteria);
  }
}

The specification looks like this:

class ProductAvailableSpecification: ISpecification<Product>
{
  public bool IsSatisfiedBy(Product product)
  {
    return product.ActiveYN
           && product.ExpirationDate > DateTimeService.Now
           && product.RemainingQuantity > 0;
  }

  public ICriteria EnsureThatWillBeSatisfiedBy(ICriteria criteria)
  {
    return criteria
      .Add(Expression.Eq("IsActiveYN", 1))
      .Add(Expression.Gt("ExpirationDate", DateTimeService.Now))
      .Add(Expression.Gt("RemainingQuantity", 0));
  }
}

Here is how it can be used in the domain:

ProductAvailableSpecification _productAvailableSpecification = new ProductAvailableSpecification();
public bool CheckFirstProduct()
{
  Product product = _products[0];
  if (_productAvailableSpecification.IsSatisfiedBy(product))
    return true;

  return false;
}

and here is how it can be used in the repository to load only products that are satisfying the specification:

ProductAvailableSpecification _productAvailableSpecification = new ProductAvailableSpecification();
public IList<Product> GetProductsSatisfyingCriteria()
{
  return Repository<Product>.CreateCriteria()
        .EnsureItWillSatisfy(_productAvailableSpecification)
        .List<Product>();
}

The specification logic is still written twice, but it is encapsulated in the same class and it is easy to maintain.