Hello.
Firstly, I am so very sorry you have been through this and lost your baby in such a difficult way 
I had a baby diagnosed with acrania last year. We chose to have a tfmr which took place on New Years Eve when I was nearly 14 weeks. Pathology showed that our baby boy also had Edward's syndrome. The consultant said that the likelihood in our case was that the acrania was caused by the chromosone problem, rather than being a standalone ntd, but she couldn't rule out the possibility that we'd managed to have both a ntd and T18 as separate events in the same pregnancy. Consequently she prescribed 5mg/day folic acid until I am past childbearing age.
I'm a bit hazy now on the numbers but I know the consultant said that by taking the 5mg folic acid it reduced the chance of another serious ntd by about 75%. Overall the risk is still slightly higher than for the general population but you are right it is around 1-2%. Unfortunately it's not possible to diagnose or exclude acrania until at least 11 weeks so we were advised that no early scan would be offered, pretty much cross your fingers and hope was what they told us.
In the immediate aftermath of loss I felt sure I wanted to try again, as much as anything, I felt this need to "prove" to nature that if I wanted a baby I could bloody well have one thank you very much. After a couple of months the bolshiness faded and I was very scared.
We did decide in May to throw caution to the wind and I fell pregnant straight away. I'm now 26 weeks and so far, so good, healthy looking baby boy. It has been incredibly difficult mentally and emotionally though and I'm under the mental health team having 1-1 CBT with a therapist to try and help manage the anxiety/depression/trauma effects. If you do decide to go ahead, please take care of you. I think therapy or counselling is a must to get through it.
For context I should add that my acrania pregnancy was my third pregnancy. I lost my first daughter at 20 weeks due to an infection, and then went on to have another daughter less than a year later - she's 5.
One thing I will say having had two second trimester losses, is that for me the first was the worst. I suspect there are many many factors at play here, but there was an element of having been through it once before so the second time I didn't experience the same profound and traumatic shock, nor was the process frightening and bewildering. In some way, having done it before made it easier for me to navigate, and that helped me feel able to try again.
I wish I could promise you it will all be ok next time. The chances are it will, but equally the chances were that it would be fine last time and it wasn't, so I completely understand not being reassured by statistics. I hope you can find your way, in time, to the right decision for you