National 5 day holiday in September...

I hear that Mon 21-Wed 23 Sept are declared holidays and when added to the weekend make a 5 day holiday in all.
What will be the likely implications to travellers? Will everything stop and holiday areas be booked solid or.....?
Please advise so we can make our plans.

What will be the likely implications to travellers?

The situation will be very similar to the "Golden Week" in spring:
http://www.japan-guide.com/e/e2282.html

Trains will be crowded especially towards the beginning and end of the holidays.

Will everything stop and holiday areas be booked solid or.....?

Almost nothing will stop. To the opposite! Everything will be open and compete to attract tourists. Popular holiday destinations will be crowded or booked out.

... and have the possibility add 2 days anual leave and you will be off work for a total of 9 days!!! just imagine what you can do and where you can go with all this time. As for me, I am considering another (short) motorcycle touring - either direction Kyoto or maybe another Kyushu / Mt Aso trip.

All this freedom for the locals could be very disruptive for we tourists!
Seriously, have you considered Shikoku? Should be great on a motorbike.