Pumps are typically considered to be rigid components when included in a system analysis so that calculated strain-based (thermal) loads will be (conservatively) higher. These rigid components may still grow thermally but they should not distort under load. Since they are not intended to distort under load, suction side response is isolated from discharge side response. If so isolated, there is not reason structural reason to model through the pump. It's up to you. It may be more convenient to do so.
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Dave Diehl