How does the giant squid affect the ecosystem?

Any predator effects its ecosystem by controlling the population numbers of the food animals. And since the animal caught is often sick or injured, or of poor genetic quality, the predator also effects the quality of animal that survives to reproduce.

We really don't know much about the giant squid or the ecosystem it inhabits.

Living giant squid have only been observed once, very recently.  Everything else we know comes from dead specimens.

They are likely very important predators in their environment, feeding on pretty much any kind of fish they want.  

In turn, they also appear to the favourite prey of the Physeter, or Sperm Whale.  Sperm Whale often bear hundreds of scars on their faces from the ragged tooth-lined suckers of the Giant Squid, obtained in titanic deep-sea battles, and the hard, indigestible beaks of Giant Squid are often found in the stomach contents of the whales.

So no one really knows what would happen to their ecosystem without Giant Squids.  We don't even know how many of them there are.