The paper does not claim that that 97% of scientists endorse AGW. The study was conducted to evaluate the consensus within the published literature, and it found that an overwhelming percentage of published papers expressing a view on the question do endorse the premise that human activity is causing global warming.
Among abstracts expressing a position on AGW, 97.1% endorsed the consensus position that humans are causing global warming. In a second phase of this study, we invited authors to rate their own papers. Compared to abstract ratings, a smaller percentage of self-rated papers expressed no position on AGW (35.5%). Among self-rated papers expressing a position on AGW, 97.2% endorsed the consensus.
When scientific findings are summarized in the popular press, things often get a bit distorted. The key finding of the referenced paper is given as the last sentence of the abstract:
Our analysis indicates that the number of papers rejecting the consensus on AGW is a vanishingly small proportion of the published research.
As to the papers that did not endorse or deny the existence of AGW, the paper offers this explanation:
Of note is the large proportion of abstracts that state no position on AGW. This result is expected in consensus situations where scientists '...generally focus their discussions on questions that are still disputed or unanswered rather than on matters about which everyone agrees' (Oreskes 2007, p 72). This explanation is also consistent with a description of consensus as a 'spiral trajectory' in which 'initially intense contestation generates rapid settlement and induces a spiral of new questions' (Shwed and Bearman 2010); the fundamental science of AGW is no longer controversial among the publishing science community and the remaining debate in the field has moved to other topics. This is supported by the fact that more than half of the self-rated endorsement papers did not express a position on AGW in their abstracts.
Some of these papers may have stated a position within the body of the paper, but the study only looked at the abstract. Many others may not have stated a position at all, as the purpose of the paper was to report on some particular new finding in the climate science field, rather than to point out that the climate is changing due to human activities. New papers published in the thermal sciences field don't include an explicit endorsement of the laws of thermodynamics.