Can an alien and a plantsim have a baby together?

Yes, but when a Plantsim has a baby with another Sim, it will never be a Plantsim. Plantsims can only be spawned (the result of your Plantsim and an unseen NPC designated as the "perfect Plantsim" - he's not so perfect in my opinion :D ) or being turned into one.

In addition to what Animirla said: in Sims 2 no supernaturals will pass their lifestate on to children (except for Plantsims spawning and aliens, which is technically just certain genes). Werewolves and witches etc will just give birth to muggles as well.

Yes, plantsims and aliens can have baby together. The baby will have alien DNA (green skin, black eyes and hair if alien has it and alien facial features) and plantsim's human DNA (Skin and hair color before becoming a plantsim, eye color and facial features).
Life state isn't something that is passed on to babies. So two vampires will have a normal human baby. However, alien features do pass on only because aliens only have green skin, black eyes and alien facial features (aliens have no special powers).