Typically with a gastrectomy marginal tissue is taken to rule out spreading. They are probably taking both lymph nodes and the spleen because those are very common places for stomach cancer to spread. You don't want to take any chances with spreading because, as most would agree, gastric cancer that spreads to the lymphatic system or the liver is sometimes impossible to treat. My dad had his entire stomach, spleen, and most of his pancreas removed and all organs besides his stomach were clear. No side effects of the removal and the recovery was the same as just a stomach removal surgery. Don't panic. It sounds like the docs are just being extra careful and are following pretty standard protocal.
Good luck.