All such spacecraft would have to do to cause massive devastation is aim at Earth and not stop, though it's likely that more advanced civilizations could come up with more effective means of destruction.
Alien civilizations could have advanced scientifically for thousands, hundreds of thousands, or even millions of years. It is unlikely that we can accurately put limits on their capabilities.
[1] - https://en.wikipedia.org/wiki/Project_Orion_%28nuclear_propu...
But as you point out, anything that can travel between the stars can trivially wipe out all life on Earth without warning. They also know we exist already thanks to the changes in the chemical composition of our atmosphere. If they want to kill us then we're dead.
The flaw in this analogy is that the you with these capabilities has different, and possibly incomprehensible desires, compared to the you who wants a Coke.
The natives of Central America and Mexico were not aware of how excited those Spaniards would be about Gold and Silver.
Such a strike might not even be that expensive or need FTL technology: just send out a few one-way nuclear-armed suicide drones at 0.12 c [1], via a path that obscures their origin (e.g. via a gravitational slingshot or three).
[1] Perhaps with a design like https://en.wikipedia.org/wiki/Project_Daedalus, https://www.damninteresting.com/the-daedalus-starship/, which is probably even within our technical capabilities. We also have weapon designs that could render the a planet uninhabitable (e.g. https://en.wikipedia.org/wiki/Salted_bomb).
Let's say an advanced civilization around Sirius wants to take us out. A chunk of metal (or anything really) of about 1000 metric tonnes would be completely invisible until it were very close. Travelling at 99.99% of the speed of light, it would impact with the energy of 13 times the meteor that wiped out the dinosaurs. The light of the projectile being "fired" would reach us in 10 years, and the projectile itself would arrive just 8 hours later. There is no foreseeable way to defend ourselves against that.
An overly cautious civilization with that kind of technology might just decide to start sterilizing all the planets in its surroundings without having to leave their solar system, just in case.
This used to be a common SciFi staple, that a civilization advanced enough to travel the stars must have solved their social issues first or they would have destroyed themselves with their own technology. Basically as the cost of ending all life on the planet drops you need to advance your ethics fast enough to prevent it from happening. Eventually everybody is carrying around pocket antimatter batteries and either everybody is well adjusted or everybody is dead.
An active weapon could be targeted at a solar system too far away for an accurate preparatory survey, then identify and target rocky planets and large artificial structures once it arrives. It could also perform course-corrections in transit, and remain substantially dormant for much of the trip for stealth and surprise.
Do you let the plane in? Do you stop it from traveling at all? Do you glass the surface of America with nuclear weapons? How do you know they won't do it to you?
Plus, it doesn't even make sense to try to "protect" yourself because their first move if they even thought like this would be to nuke everything flat with no warning. There's no defense against it. You can't hide either, the signals are already out there, they know where you are.
It makes no sense to insist that aliens would think as you think they should. That doesn't even make sense for humans in most cases.
> You can't hide either, the signals are already out there, they know where you are.
That's arguably not true.
We are on the cusp of being able to detect the biological markers of life on distant worlds by spectroscopy. An alien civilization that can traverse the enormous gulf between solar systems can very easily build widely spaced telescopes that can monitor all nearby solar systems for changes to atmospheric composition. Anybody who is paranoid enough to need to kill any life around them would obviously build such an array. There is no hiding from them, the technology is much too simple compared to what you need to travel between solar systems.
Maybe they can't themselves, but don't like the idea that someone else eventually may be able to.
I think you're overconfident of the safety of actively advertising our presence to the universe because you're making a lot of assumptions and only considering a small number of possibilities. The problem is that there are so many unknowns and so many shades between different possibilities that no one can really be confident about anything, except that the risk could be anywhere between zero and the maximum.
But you can imagine a situation where like we’re looking for life on Mars and in doing so inadvertently destroy unknown life.
Its like you are thirsty so you build an intercontinental jet plane from scratch using parts from around your house to fly to Japan to steal a single Coke from a 7-11.