For people who say, "rather not", why not? Is it because it goes against your ideas of how space should be like? I don't mind if you disagree, but at least provide some reasons why.
I, too, would rather not.
But if it's like what you said and the monsters are at least fairly interesting, then it might at least be tolerable.
If it's like it is in Moo2, with space dragons and space eels and space amoeba, I'll mod it out.
Cardboard cut monsters and lazy implementation can make it cheap, but is there any underlying reasons why you don't like the idea? If you are looking for moral justifications to kidnap and drug the devs, then I'm sure there are plenty of others you can find
Distant Worlds did this, mostly to provide some early game threat before finding other alien species and culling potential expansionism a bit.
Whether it should be done or not in Stellaris is another question. The large, decadent empires probably took care of that giant space monster business with whatever highly advanced all-destructive arsenal they have/had. But still, the idea sounds fun and if done well it could provide for some nice quests. Would you want to kill it and burn it with nuclear fire or research while it's alive, somehow working towards controlling it?
In Stellaris, we don't start as large decandent empires. However, if you are talking about previous empires that have been eradicated for whatever reason (ancient early alien civilization trope), then there could various reasons why space organisms still exist. Maybe, the former empires kept them under control to use for their advantage. Maybe the organism evolved due to reasons related to the ancient empire's eradication. Maybe the organism's existence is owed to the ancient empire... or its eradication. There's plenty of reasons why we can call them into existence.
Also, there's no reason to automatically assume that giant space horrors or organisms will always be trumped by developed humanoid technologies. It could be, that people simply learn to adapt, and live around it, or maybe even learn to work in symbiosis, rather then directly annihilating them.
They may even learn to live with such threats for a large chunk of their space-faring history, much like how we all come to live with a reality where there are earthquakes, meteor dropping, and strange men entering your house at night to "mod your game". Perhaps the day will come, when they will be able to obtain the technologies to truly eliminate the creature, but it may come with a price. Especially, if there has been a developed symbiotic-like relationship.
I would say that such organisms may not necessarily even have to be 'encountered' during space travels. They can be something that an alien civilization have been exposed to even prior to their space faring history ("Look, it's a plane, no it's a bird... oh shit it's a giant dong! run for your lives!")
Well, space-dragons are just a bit lazy. However, with a bit of thought I'm sure the good people at Paradox can dream up a few varieties of "giant space monsters" that seem plausible enough (at least for a setting that assumes a variety of intelligent species mysteriously achieving FTL at that same time). Giant monsters don't have to be biological or if biological don't have to be natural.
I hope the galaxy is full of weird, wonderful and horrible threats and at it would be disappointing if at least a few of them weren't giant-scale.
My thoughts are the same.
I don't think such creatures should be common, but they should at least exist, and offer a fair threat when encountered.