We didn't have a hole in the heart, but did have another soft marker giving us a higher risk of Down syndrome or another chromosomal disorder. We declined the amnio at that stage as we felt that it the extra information didn't cancel out the risk of the amnio, but it is a very personal choice. Even though we declined the amnio, we were treated as higher risk and so had extra monitoring, one of which was an echo scan done by a cardiologist at the main children's hospital here, plus more frequent scans to check on the baby. Maybe see if this is an option if you don't want to do the amnio. We ended up having an amnio at 28 weeks but that was due to a complication with our little one's lungs. At 28 weeks, the risk is pre term labour as opposed to miscarriage, but we had thought we would be delivering at that point anyway .
I'm sure they've explained it to you, but just in case, the reason they will have suggested the amnio is that between 50-60% of babies born with Down syndrome have a hole in their heart (an ASD or a AVSD), but it is fixable by surgery.
If you decide to go ahead with the amnio, and you haven't already been referred to the maternal fetal medicine department at your hospital, it's worth asking for a referred. These doctors are really experienced at doing amnios and so their risk levels are quite low.
Good luck with everything.