Does GreenGuard Certified Products Qualify for IEQc4.1-4.2 ？

There are certainly GreenGuard-certified products that qualify for IEQc4, but to earn the credit you have to be able to document VOC content, not emissions. So you need that content number, which GreenGuard does not provide.

Due to CA 01350 being the compliance path in schools, we have seen projects that submit the GREENGUARD Children & Schools certification (and laboratory test reports proving compliance) for their paints & coatings and adhesives & sealants and they receive credit in EQ4.1 & EQc4.2. So products that prove that they are low-emitting by showing compliance to CA 01350 can be utilized as a way to garner credit.

CA 01350 EMICODE goes for testing of emissions from applied paints, coatings, adhesives and sealants into indoor air and gives results as emission factor (µg/m2h) or as air concentration in a model room (µg/m3).
US VOC limits for such products go for testing of VOC content in a can of non-used liquid product and gives results as g/l.
There is no correlation between both - except if there is absolutely zero VOC content, then nothing can be emitted.
But no VOC emissions after 14 days do not tell you anything about initial VOC content in the can. I agree that VOC content in the can is no measure of product quality with respect to indoor environmental quality, but present credit laguage is written in such a manner.
Hopefully this issue will be overcome with LEED 2012.

With respect to CA 01350 compliance for a water repellent ceramic tile floor coating, the product does not comply with the water repellent g/l limit, but is SCS Indoor Advantage Gold certified.

According to the SCS literature, that certification complies with the CA 01350 requirement. So will this product comply with the CA Health requirement by virtue of the SCS certification even if the g/l content does not comply with SCAQMD 1113?

SCS Indoor Advantage Gold does show compliance to the CA 01350 requirements of minimizing 35 VOCs. So this product would comply with the CA 01350 requirement.