There's a relevant interview with the director, Richard Linklater, co-producer Tommy Pallotta, and others over on Animation World Network: ("'A 'A Scanner Darkly': An Animated Illusion. In it he shares his"), in which some thoughts are shared on the reasons for the artistic decision, as well as some of the associated pros and cons of implementing these effects:
My personal feeling is that thean adaptation of this story, while excellent, would not have appealed to a broad enough audience without a "gimmick". This is a drug movie - which may be alluded to in the article, where it states Pallotta believed the film would not have been made had it not been for the animation element.
The characters are losing their ability to perceive their immediate reality, and it's difficult to imagine how this infliction would have been otherwise conveyed in a visual medium, without the use of effectsresorting to choppy exposition showing what a person thought they were experiencing vs what was really happening. If narration or dialog had been used, it's unlikely the experience of the Substance D users would have held the audience's interest.
On that note, Bob Sabiston's "Rotoshop" software, which was used to create the visuals, was also used for a series of advertisements around the same time. While not directly related, the writer of those commercial spots offers the following perspective on the effect:
Somehow washing out the real-world details present in a live actor's face and in an actual background set lets us move past what we're seeing and shifts our attention onto the dialogue.
... Which would have been great for this sort of character drama, though for myself I found the visual distortions distracted me from the story.
As for whether money plays into it (beyond if the film had never been made), the first article also discusses this along with some of the pros and cons of the animation:
They were also able to spend less money on the live-action shoot, such as with set decorations, because they knew they would be able to enhance the look later in the animation process.
An article on the LA Times("[A long way from Disney][3]") expands on this:
In mid-2004, Linklater shot a live-action film on digital video [...] He finished in about a month, partly because he didn't have to sweat the small stuff.
While the filming itself was cheaper, it goes on to explain that the process of animating the film led to increased financial costs:
[...] by the end of 2004, the film's producers became concerned that his team wasn't progressing as fast as they had hoped.
The producers had based their schedule on that of "Waking Life," said Katy O'Connor, then the film's lead animator. That was unrealistic for "Scanner," which called for a more uniform visual style, used twice as many frames per second, and featured more complex shots with more camera movement, more action and richer backgrounds.
Linklater and co-producer Tommy Pallotta believed that a team of 30 animators could finish the film in about six months for a budget of $6.7 million.
In the end, completing "Scanner" required up to 50 animators, took more than twice the time allotted and cost more than $8 million.