Decrease in Surface area leads to Increase in load capacity for mesoporous material?
Although I only have access to the abstract of the link you provided (unless you want to spot me $40 ;) they have characterized their glutaraldehyde-functionalized SBA-15 surface using at least 7 different analytical techniques, so I'm pretty convinced that the surface area, pore diameter and hydrophobicity are as they say.  

The ~50% increase in surface adsorption in spite of the 13-fold decrease in surface area just illustrates the fact that surface adsorption is a function of two parameters: the affinity of the compound for the surface in question and the area of the surface available for adsorption.  It seems that for the system you've described, these two parameters simply switched from high-surface area / low adsorption affinity to low-surface area / high adsorption affinity, with the adsorption affinity "winning out" over the decreased surface area.