You are right to be concerned that employers will be afraid to hire you because of your diagnosis, and an unfortunate consequence of the Americans with Disabilities Act (if you are an American) is that they will not be honest about this with you. The worst case from their viewpoint is that they hire you, find you don't fit in, but then are told they can't fire you because doing so would constitute discrimination. To combat this consider offering to first take a temporary part time or internship position so they can get to know you. My guess is that the first sentence of your post would greatly concern most potential employers.
I'm not sure about the timeline of your employment gap, but you might be able to use the fact that you have a special needs child as a justification for it.
There is a reasonable chance that your current employer assigns a high probability to your having autism because (a) of your behavior, (b) being told that your daughter has autism got them to think about autism and connect it with your behavior, and (c) someone realizes that your daughter having autism raises the probability that you have it.
My autistic daughter is also intellectually disabled. She needs lots of special care, often on a difficult-to-predict basis. It was especially so in the first years following her official diagnosis. Not sure if it's a good thing to mention this, though: I'm afraid the employer could take this as evidence that there's a significant risk that I could some day descend into a poor productivity phase (or even another leave, at no notice). It may also be the case someone could take all this as a positive, by correlating it to a potential underlying disposition or motivation to hard work and responsability, but it seems better not to count on the possibility that this effect could override the first one.
An option would be to tell employers that I was on a leave to take care of a very sick family member (say suffering from the illness I suffered from) that since then has been definitely transferred to a special care facility, while trying to "fill" the gap with some skill-sharpening/expansion activities I did during the period. Classical example being online courses directly related to my main career path. Unfortunately it was not the case, as a I took online courses on online education, while planning to apply for typical engineering jobs. It's still something to show for that time off. I can try to make it applicable - e.g. I can relate it to being able to gain a skill to train others or take team leadership if necessary, or find ways to train people in other offices without having to travel.
Current employer is aware of my somewhat extraordinary circumstances involving both, being a father of a disabled child (my autistic daughter is also intellectually disabled and needs lots of special care, often on an unpredictable basis) and suffering from anxiety disorders myself. The employer was able to offer special working conditions regularly (e.g. working from home during a crisis).
You might want to try a mixed strategy where you reveal different information to different potential employers. Since you only want one job, you would likely gain by this variance increasing strategy.
Don't do it if you need money. It isn't that they are going to associate the gap in your resume with your condition (Currently Employed at Comparable Job is the gold star of resumes, nothing else matters nearly as much), its that they will DQ you immediately.
You work against this at your NGO, you know how real this is. If you google an applicant and you get mental health stuff its in the same category as "sued last boss" or "felony conviction". Dealbreaker.
Your profile states your location as Brazil. That means anything that somebody says that might be true for the US might not be true for Brazils job market.
In case you haven't already posted there, the Wrong Planet forum might give better help with this problem.
If you think you will be let go from your current position in the near or mid future, start looking for a new job now. I'm not sure whether you will gain anything by disclosing your condition, vs. having the unexplained gap. Don't lie outright, of course. Can you say that you paused your studies to care for your child, without mentioning exactly what's going on? Your plans to return to grad school are a mark in your favor - that could also be a stated reason to switch jobs (i.e., "I want a job that will support me doing night school/ flexible hours for a year or two while I get even smarter").
Also, you have a Master's in EE. I'm guessing that's a field where there are far more jobs that qualified applicants, like basically all forms of engineering. That, plus the fact that even neurotypical engineers are really weird, and I wouldn't expect things to be too bad on a job hunt.
Background
A few years ago I (was forced to) left grad school (halfway into it) because of complications related to a set of anxiety disorders (a typical comorbidity in Autism Spectrum Disorders; I now have a Master's degree in Electrical Engineering. I'm also planning to return to grad school next year).
I have a family (2 children). Around the same time I left grad school, we received my daughter's diagnosis (she has more of a classical form of autism), followed by my own diagnosis.
With regards to my professional record, after approx. 2.5 years in grad school and 2.5 years completely out of the job market, I finally began to work at a small consulting firm. They are aware of my daughter's autism, but they don't know of my own diagnosis.
NGO
I'm also vice-president of a local, small, autism-related NGO who is now trying to convince me to disclose my being on the autism spectrum (for publicity and awareness reasons). They are planning to arrange an interview for me at a TV channel. In fact, the decision was already made, as I'm effectively coming out of the closet on December 9th, by means of an interview on a local radio station.
I'm enthusiasticaly in favour of such a move (for both egoistic and altruistic reasons), but am also afraid of potential consequences on my future professional prospects. Also consider that it's likely that I will need a new work position very soon.
In summary, I'm only worried with the fact of also having a track record of being out of the job market for quite some time, so that I'm afraid some hiring manager could be tempted to negatively associate the gap in my resume to my condition.