I use only hand tools and no premade parts.
I work almost in similar conditions as you.
My studio is 3mx3m and just a room in our house, a place where I practice,
make arrangements, prepare my teaching etc. etc. + make guitars.
I do all the guitar building in the studio but not the final sanding
(as Michael points out), which is done outside or in a shower room,
depending on the season.
I have a very good indicator if everything is healthy or not - my wife.
She has asthma and several severe allergies.
No problems so far.
But I have to be very methodic.
Here it goes:
My tools are a tablevac and an aircleaner - a good quality one (1100€),
I have it always on while working and one hour after.
I put a sheet under the wood when sanding or planing and frequently empty it by gathering all the shavings
(also them on the floor) into a plastic bag and then I use my tablevac.
When days job done I go out shake the sheet clean, sweep the surfaces (working table and areas close to it) clean,
vacuum and go over surfaces with a damp cloth.
The plastic bag should be binned at this point, specially if I've worked with tropical woods.
After a guitar is made I clean the entire room very meticulously.
And of course the aircleaner must be cleaned when necessary.
Other thing is that I try to make all my movements as smooth and economic as possible
in order not send a cloud of dust in the air while working (or cleaning).
This might sound like a lot but when you get hold on it, it is not.
Cleaning shavings + vacuuming when planing takes only 2 min./hour.
Cleaning each day takes 5 minutes.
Final cleaning after job done (guitar is made) takes 2 hours.
And IMHO minimizing the movements while working makes me better builder
as I don´t understand guitar building to be something that happens in a sawdust cloud
where you try to avoid that flying shavings don't knock you out.