Depends are they going into a hostile situation or are they going to a starbase. No one is going in with peaceful intentions when there are a bunch of Klingons holding federation scientists hostage. Though having a holster/unholster toggle would be nice. Maybe that is why Sulu always looks so nervous when i pay him a visit.
I think when your asked to beam down, you should have a check box for with weapons draw. That way, if you want your weapons out on landing, they are.
if it could remember my last choice... but I doubt they would clutter the npc window with checkboxes and such. also it makes sense to beam down on assault missions with weapons drawn. there were episodes where they beamed out with weapons drawn I think.
edit: also im guessing they would do this at some point but didn't have the time