Just saw UA900 (747 SFO to EDDF) going over SF bay with wheels still up. Any normal reasons for that ??
probably to cool the brakes, its normal
I’m assuming you mean the wheels not up after 6 minutes. I agree that it can be for brake cooling but 6 minutes is a long time for that.
Would a flight still be over the bay after 6 minutes anyway ?
If they departed 1R and flew over OAK on the Linden departure, no. maybe 2 minutes. Departing 10 and making the left turn to LIN adds maybe another minute or two and usually takes you east of OAK by a few miles.
That seems sort of weird to me, aside from using the brakes to maneuver for takeoff, I can’t imagine there’s that much heat build-up to necessitate hanging the laundry out.
On large airplanes the heat buildup can be immense especially when taxiing downhill for any length of time. I talked to an A300 freighter crew in Paris one time, from their ramp to the primary runway is about 15 minutes, all downhill. They quite often have to pull over in the runup area to let the temps. drop to whatever the maximum is. The said when they are heavy and the outside temperature is hot it can sometimes be 10 minutes. You don’t want the heat buildup to continue with the gear up and the doors closed so it is not uncommon to leave the gear hanging, not for 6 minutes though.
Yep, I did mean wheels not up 
Most of the time the heavies headed to Europe take off on runway 28 and head out over the ocean, then they bank right and come back over the golden gate heading east. Watched planes come over for years and first time I ever saw the wheels still down.
Back in April I saw a KLM 747 leave them down for about 2 minutes.
A few months ago, a United plane took off from SAN and advised the tower that they would be leaving the gear down for around 10 minutes, due to some kind of maintenance procedure. I can’t remember if it was an A320 or a 757…But I thought it was a little interesting.
I saw this the other day with a FedEx A310 at EWR. Took off to the South, then turned West with gear still down for a good 3 minutes. There really isn’t much of a downgrade from the FedEx ramp to runway 22 so it may have had to do some heavy duty braking for some reason.