RetireJapan

I used to invest regularly into Vanguards VOO index fund, which I believe is traded in USD.
All my money I want to invest is in Yen and I now trade via Interactive Brokers Japan.
Given the current FX rate - is it a terrible idea to invest in anything priced in USD and I should stick with Japan stocks?
My investments are all long term, 10+ years

I think you are essentially asking whether the yen being weak now is an indication that it will get stronger in future, versus the US dollar.

I am investing my fresh yen in foreign securities.

I do regard the yen as being in a multi-year downtrend, so feel completely comfortable selling it for foreign assets.

That said, if I did think the yen were going to appreciate, I would go for an outright forex trade to express that view. Foreign stocks will keep earning dividends and growing otherwise, over your time horizon

If the yen is going to switch back to an appreciating trend, I think there will be a significant catalyst that will suggest that to us. I am sure it will be a big topic here on this forum should such a catalyst be revealed by the rulers! (Adopting policies more akin to the Swiss than those of Abenomics, for example, would probably have me sold.)

But if one is concerned about the possibility, investing in some domestic Japanese stocks would make sense. Diversification is a fine approach.

Just to offer a slight counter-argument, I personally wouldn't feel comfortable investing a lump sum in the S&P 500 right now using yen. The BOJ don't like USD.JPY above 150 and it is getting close to that level again. Some analysts think they will announce something in their July meeting which will cause the rate to drop somewhat. Others think they will wait until September. The latest FXStreet survey of about 30 analysts and experts puts the average rate at 136 at the end of Q3, which is only about 6% down from now but would present a better buying opportunity if it happens (remember the "experts" are not always right!). What's more, there's historically been a positive correlation between USD.JPY and Japanese stocks, so investing in them might not provide much of a safety net if the yen strengthens.

Having said that, I agree with sutebayashi that the long-term trend of the yen is down, and it's not a bad idea to ride it until there's a clear signal that the trend will change. The problem is that markets trade expectations and tend to be one step ahead, so timing it might be tricky.

Actually a lot of us will be in this situation in January if the yen is still weak, wondering whether to lump sum our 240 man (2.4 million) new NISA allowances into global stocks, or DCA them in chunks.

And by the way, my opinion above refers to large lump sums. I think that investing smaller amounts of yen regularly in foreign markets isn't a problem and should be continued whatever the rate does. I'm personally doing that in our iDeCo accounts.