A month with 1 year visa - can i go home?

I'm a Filipina married with a Nikkeijin. I arrived last June 4 and we just found out we are 3 weeks pregnant. I wanted to go home to the Philippines so badly. My morning sickness is getting worse everyday. I've lost my appetite and I couldn't even drink water because it makes me wanna throw up. My question is: is it okay if I go home? Or are there any chances that I can no longer come back to Japan after giving birth since I only stayed here for a brief period of time?

It is not at all a problem to leave Japan before your status expires.

Won't they question me once i renew my visa? I heard they are getting stricter now and there might be a chance i'll have to go back from the first process: request for a new COE.

You mean you want to stay in Philapines until after your visa expires? If so yes you'll have to apply for a visa again. If you plan on returning before you visa expires, then you just apply as normal for a extenstion/new visa.

What what about your husband? That is not fair on him for you to run back to the Philapines.

You should be able to temporarily leave Japan under your visa and return within a year (and before the visa expires) without having to start all over again.

In this case, temporary might be a few months or nine/ten months.

That would involve flying to Japan with a one- or two-month-old, not sure if that's a good idea.

Agree with Firas, you shouldnt be flying if you are pregnant. Even post-pregnancy takes awhile before you board a plane.

Won't they question me once i renew my visa? I heard they are getting stricter now and there might be a chance i'll have to go back from the first process: request for a new COE.

It shouldn't pose a major problem as long as you return within the limits of your current residency status, but it depends how much time you end up spending outside the country. If you go over your residency duration you'll have to reapply from scratch.

As for travelling while pregnant/with newborns, most doctors recommend avoiding air travel during the final trimester and especially after 36 weeks. Travelling with newborns is typically best avoided for the first three months.

If the baby was born outside Japan, you'd that cause any effects on visas also? Or resident status of baby?

Place of birth does not matter..
Why don't you explain your situation to immigration and get visa extension done before leaving Japan