It'd be interesting to know if children who start this way develop a different way of thinking about playing (though I see from http://en.wikipedia.org/wiki/Suzuki_method
that there's probably already a lot of literature about it).
There hasn't been as much study as you'd think... because individuals will vary in ability and practice habits, it's rather difficult to form a broad assessment. Every criticism I've heard boils down to anecdotal evidence.
I don't use the "Suzuki method" for guitar - in my opinion, it's a re-hash of the violin method, and the instruments present different problems to the performer. But I do use some of Dr. Suzuki's teaching methods, gleaned from both his musical materials and the biographies of him and his school.
Criticisms of Suzuki fall into two main groups: 1, that learning by ear delays and/or inhibits the ability to read well. 2, that Suzuki's emphasis on group performance hinders individual musicianship.
For criticism 1, the same is true of guitar tablature, or the methods which stress "learning by ear". Music is a language, and a complex one; the ability to play is not dependent on the ability to read, or vice versa. Neither are they mutually exclusive. I feel quite strongly that reading standard music notation will not hinder developing other musical abilities... and that the ability to read is essential to fully understanding some aspects of music.
But there's also a reason we don't teach reading comprehension to toddlers. It's quite possible to 'speak' music without reading it - in fact, the vast majority of guitarists do that. While it's true that learning to read after you learn to play requires a step back, that doesn't seem to hinder children - perhaps because they are learning new things all the time, and consequently have a beginner's mindset to new skills. While an adult who can shred will often be bored silly (and frustrated!) by trying to tackle reading "Twinkle Twinkle, Little Star", children find joy in acquiring a new ability.
Over the years, the students I've had who most fluently read music were those who developed their musical reading ability at the same time
as they were learning to read words. Both skills are the interpretation of written symbols, and they seem to support and supplement each other (much as bilingual ability is more pronounced in people who learned a second language early on). I have two students now who are 12; both started reading music at age 6. Both read fluently in all positions, and up to five accidentals in the key signature.
All of the American Suzuki string instructors I know supplement the Suzuki material with other methods by grade 4 (of 10). No method is complete, and individuals have different goals and learning styles. That's why I use several different methods with my students, and supplement with other materials.
I don't think the second criticism of the Suzuki method applies to the guitar. Although most contexts use guitar in a solo or duo combination, most also require working with the ensemble. So while it may limit your ability to wring out all the possibilities of a cadenza... how many guitarists need to do that? I think it's far more important for the average guitarist to be able to play with others!