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This may be an obvious question, but I don't know, which is why I'm asking here. I've searched "Canberra canopy porthole" and "window", but didn't get any information. There is a porthole of sorts on the left side of the canopy of this bomber, I'm wondering what it's for.

Photo source.

Here is a view from inside the cockpit:

Photo source.

There also appears to be a similar thing on the bottom of the nose of the aircraft, offset to its right. The following is a screenshot from a video game, as I wasn't to find a photo of this.

I'm tempted to say that this second one is to do with bomb sighting, however if it weren't there, the bomber would have just as good a view, wouldn't they? Also, as from what I've seen the bomber sits quite far back from the front of the nose, it seems the bomber would only be able to look forward at shallow negative angle, essentially not much different from looking in front of them.

It's called a "Direct Vision" (DV) window. The canopies are sealed shut, so the small DV window is provided as a way to open a small hole if required. For example, to communicate on the ground or in the event of icing or other canopy issues.

Edit: I wasn't able to find a formal source, but this page is fairly authoritative:

http://alverstokeaviation.blogspot.com/2016/08/english-electric-canberra-technical-tour.html

Re the upper "porthole"-- it sure looks like a heated panel for clear vision in extreme icing. Note the resemblance to a "hot plate" in King Air etc. It is undoubtedly glass and can be heated by a heating element (note the wires) to much higher temperatures than the perspex canopy could tolerate. Note that there is one on each side, and this aircraft has side-by-side seating in the cockpit. As has been noted in another answer, it appears to have a hinge and a thumbscrew latch, so it could be opened if needed (e.g., a/c is heavily iced up and electrical power has been lost or can't keep up with the icing-- or just to talk to someone on the ground.)

Your question also references the flat panel on the transparency on the lower part of the nose. It is not clear from the photos whether this is heated or not; it's almost certain that this larger flat panel could NOT be opened. However you'll note that it is very common for aircraft to include a flat glass panel for aiming a bombsight or as a window for a camera in the case of a reconnaissance aircraft. The curved perspex of the rest of the transparency will always have some optical distortion. Note that until fairly recently, many fighter aircraft had a flat windscreen in front of the pilot. Again part of the reason for this was to prevent optical distortion as the pilot looked through the gunsight. If this weren't an issue, the thick armored flat glass of the windscreen could have been "faired" more smoothly by an additional curved piece of perspex in front of it, but this was only rarely done.