Have you ever wondered what "Upper" means in the context of roads? Upper Serangoon, Upper Thomson, Upper Bukit Timah are a few of the more well-known examples. In the same vein, what does "Lower" mean?
It does not refer to the latitude of a place. Lower Kent Ridge Road is north of Kent Ridge Road and Lower Seletar Reservoir is north of Upper Seletar. However, many of the major Upper places are further north eg. Upper Thomson, Upper Bukit Timah, Upper Changi, Upper Paya Lebar, Upper Serangoon. Nevertheless, many roads are named "North" or "South", which more clearly refer to their position, so it does not make sense to use "Upper" to indicate latitude.
Perhaps it refers to the distance from the city centre. This is certainly valid for most of the places, and very striking when we zoom in on the "Upper" roads in the heart of the city: Upper Pickering Street, Upper Circular Road, and Upper Cross Street. These are no doubt right in the centre of the modern city, but a little further from mouth of the Singapore River than their namesakes. One imagines such a conversation when the river mouth was a bustling port:
"Deliver his cargo of tea to Lee's warehouse."
"Where's that?"
"Just a little further up Pickering Street."
On the other hand, Upper Aljunied Road and Upper Bedok Road appear closer to town than their respective "ordinary" roads.
This leads to the best explanation. The "Upper" areas happen to be further away from the city because the suburban areas are on higher ground. "Upper" must refer to higher ground!
I feel your indignance (you must have just muttered "duh"). But it is not so obvious when looking at Upper Changi Road relative to Changi Road, or Upper Serangoon Road compared to Serangoon Road. But it is very obvious comparing Lower Kent Ridge Road and Kent Ridge Road. The clearest indicator was Upper Bedok Road, a small dead end road that leads up a small steep slope in Simpang Bedok. Upper Bukit Timah is noticeable in this respect as well.