I've run out of yen...

I going Hakone tomoro. I've run out of yen.

What time does money changer open? Are ther any at UENO JR station?

Is it worth it make a trip to hakone at this time? or is it better to go Matsushima area or AKITA area?.. Can I use credit card to purchase the Hakone free pass if required?

If you have run out of money don't take many longer distance or expensive trips! Makes sense to save money?

Any case:
Yes the Odakyu Sightseeing Service center where the Hakone Free Pass is sold takes credit cards.

You could try withdrawing money from an ATM, otherwise if you need a currency exchange place, I don't think they open until mid-morning.

all the 7-11 have ATM taking foreign bank cards.Caution: I checked to make sure that they accept cards from the Cirrus and/or Plus network. Can't remember if it is both or only one of them as my cards work with either.

7-11 ATM is the best way. 24/7 365. So great for foreign travelers!

In Ueno, there is a place called Daikokuya that offers great exchange rates and usually is opened everyday except major holidays.