1) On the paizo.com PRD, they are not with a *(star), so they can be the only improvement without a *(star) on it. On another SRD website, they have a * (star).
...
So is the * really there?
In general, barring errata/FAQs, published book > Paizo PRD > D20PFSRD. However, in this case the book (Ultimate Campaign) is in agreement with the D20PFSRD site in the inclusion of the asterisk (*) when listing the Aqueduct* so it seems the Paizo PRD has the incorrect info.
2) Most of the bonuses are per hex, but the +1 to Loyalty, +1 to Stability per hex is really something different than the other bonuses. If the Aqueduct can only be the only non-star building on it, it would be on par with the Quarry, Mine and Sawmill to have the bonuses per hex.(+4 loyalty +4 stabily for a 4 hex Aqueduct) But if it is considered with a star, so buildable with a Quarry, Mine or Sawmill, it would be similar to a road (+1 economy/hex) to have it give bonus for multiple hexes(+1 Loyalty +1 Stability for the whole group of consecutive hexes that start in a mountain and end in a settlement).
The text: A finished series of Aqueduct hexes must connect to a hill or mountain hex (with a river or lake) on one end and a settlement on the other end; otherwise, you do not gain its benefit seems to indicate it is the series that gives the bonus. Is it right?
The effect of an Aqueduct* is listed as "Loyalty +1, Stability +1, allows settlement to build water-dependent buildings," meaning that those benefits are per hex containing an Aqueduct*.
The quoted text about not gaining the benefit means that if you're series of Aqueducts* does not start in a mountain hex with a lake/river and end in a settlement, it gives you no benefit, not that it's benefit is per completed series regardless of number of hexes making it up.
So if you have a mountain hex with a river/lake with two hexes between it and your settlement's hex, you could build 3 hexes worth of Aqueducts* and be gaining 0 benefit until you complete that final Aqueduct* and start gaining +4 Loyalty and +4 Stability per turn, in addition to being able to build water-dependent structures.
3) A canal effect: Settlements in a hex with a Canal treat the hex as if it had a river. means what exactly? What of the following is true?
A) The settlement can have a borders made of water, and parts of the grid as water. (Then have the associated buildings over them: Bridges, Pier, Waterway)
B) It should be more: Hex Improvements AND Settlements treat the hex as if it had a river. I don't see why you could have a Mill (water current), Pier(small boats docks there), or even a Waterfront(Fleets might dock there) but not use the water to irrigate farms in the hexes that the canal passes through. You could also 'seed' Fishes in there and build Fisheries over time. (I know some present time Canals and artificial lakes offer the amnesties to fish on them.) (even more if a river connect to it, I don't see humanoid blocking the passage of fishes)
C) They can use the only building I specifically see for that use: Foundry Special Increase the Economy and BP earned per turn by 1 for 1 Mine connected to this settlement by a river or Road. But then, can the mine be only connected by a canal? Or does it need to be connected to a river connected to the Mine? Isn't a canal easier to navigate than a river?
D) They affect the road construction on the hex a canal passes through by doubling its cost(Bridges). Witch is logical, since the canal must be passed over multiple places, since the road is all over the hex.
E) They affect the hex the same way a river does: +1 Economy/4 hex, +1 Stability/8 hexes. A canal should be considered as a river for navigation, trade, faster and easier transportation of some materials/equipement.
RAW, the Canal* would be treated as a Waterway in the district(s) of that settlement and count as a water district border, allowing you to build a Bridge, Foundry, Mill, Pier, or Waterfront. With GM permission, it could also function as a Moat. So, A) is the closest candidate.
B), D), and E) are how I would use it in my game and what I believe to be the RAI. For all intents and purposes, a canal would be treated as a man-made river, providing you with +1 Economy for every 4 Canal*/River hexes claimed and +1 Stability for every 8 such hexes claimed, requiring you to double the cost of a Road* in a hex that contains a Canal* to include the cost of Bridges*, allowing you to build a Fishery* in desert, hill, or plain hexes containing a Canal*, and allowing water travel through your kingdom per the rules on page 172 of the CRB.
As far as C), RAW I believe the last hex containing the settlement could have a Canal* instead of a river but I believe the river would need to connect the rest of the way to the Mine. Not the way I would play it myself, but that seems to be case.