YANBU... you may not have been with your children who do have invisible disabilities but how does that woman know that? By its very definition, invisible disabilities are not ones you can see whether or not people have, and yet the woman walked over and without any kind of interaction with you, she made the assumption (wrongly) that you were NT because she couldn't "see" your invisible disability. Not to mention the fact that just because you may not have had your children with disabilities with you right there and then doesn't mean that they don't exist.
If I was there with my NT DD, I would also want to have checked out the installation, not for myself or her, but to see if it was something I could use if out with my nephew who has ASD. Or I could check it out in order to pass on the information to my SIL so she could look into using it with her son etc.
Personally I would write to the museum or the organization that provided the installation (if it is another company and you know who they are) not necessarily to complain but to make them aware of your experience. You can write to make them aware that you, as a patron with Asperger and the parent of children with disabilities (even if they weren't with you in that particular moment-perhaps because you couldn't be sure they could cope with a museum trip because of their disabilities!) , went into the pop up installation to see whether it was something you/ your children could benefit from (maybe you would bring your other two children if you knew there was a sensory safe space for them if it got too much) and to find out more information, whereupon the female attendant summarily dismissed you as "not looking like you had disabilities" and walking away.
Now, you're not wanting her to come up and start interrogating you as to your/the childrens' disabilities either but it would be nice for her to not make uninformed assumptions without at least giving you the opportunity to speak to her first, considering she is in charge of an installation that is geared towards people with sensory issues that may not be immediately obvious. Perhaps if she had given you the chance you would have volunteered the info that you had children with disabilities at home and had your own invisible disability and so we're interested in more information, but she didn't give you that chance and you didn't get chance to get any information/leaflet/flyer etc because her assumptionson meant she dismissed you and didn't allow you a chance to get them from her.