@Wobbegong_th please see below
- What facilities are there at Jakarta airport to do during those long waiting time?
Not much at the Jkt intl airport.
- Is there a 'Left Luggage' facility that we can put some of the luggage away if we want to go outside of the airport?
Yes, tho I've never used it
https://soekarnohatta-airport.co.id/jelajahi_map/100
- For our waiting time during the outbound flight (about 5-6hrs) - is it worth to go outside of the airport, may be into the City?
There is a train going into the center of the city. If you're energetic I think you could try it, the train is quite reliable and fast. I don't remember how long it took about say you allocate 2 hours to the roundtrip, then you'll have around 2-3 hours in the city center. The train takes you to the 'kilometer zero' of Jakarta, right smack central, and a walking tour is possible (good pavements etc).
- For the Inbound flight, which we have about 16hrs to wait, we're looking to get a room at nearby hotel. Any recommendation? (preferably hotel with free shuttle transfer)
Is this in Jakarta? If yes, my office uses the Swis Belhotel near the airport, I believe they do have free shuttle. Most airport hotels are. But even if you have to take a taxi, it's quite cheap (under10USD). Alternatively, you could do a left luggage service and take the train into town and stay in town. There's a couple of good hotels very close to the airport train station (walking distance). If you try this, let me know and I can give hotel recs.
- As our target destination is Lembeh, how long is the overland travel from Manado Airport?
It's been a while since I went to Lembeh, googling says around 90 minutes and that seems right. You then take a boat ride. I don't recall this being long, and the view is interesting.
Hope this is useful, have fun!