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I like to think
The explosion was local and destroyed the base and its surroundings. Don't remember seeing the ship in Aliens so if it was out of sight, there might have been enough distance between the ship and the base to withstand the blast.
The ship was discovered after the humans were done terraforming and building the base. Propbably small groups went out to check the rest of the planet, found the ship, couple of people got facehugged, brought back to the base and the shit starts. After that they experimented on facehuggers.
Ripley leaving happened quite fast. And after that she had to deal with the queen. So there already could've been some distance between them and the planet so too far to nuke? Can't remember if they said the ship carries nukes.
We could also say for the sake of unofficial sequel, that you need launch codes. Because the company doesn't want unauthorised destruction of things they might have a use for. Like a huge alien spaceship.
Now someone make this sequel!
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