Why convert benzoate in soda to benzoic acid for spectroscopy experiment? I did an experiment where I analyzed the amount of caffeine and benzoate in soda via spectroscopy. I've got the absorbances and did all the math for everything, but I'm having a hard time figuring out why we had to add an acid to protonate the benzoate to form benzoic acid before running the spec.

I've been able to find many similar procedures and many with various pre-lab questions, but none seem to address the reason for the conversion from benzoate to benzoic acid. Here is one such procedure: UV Spectroscopic Analysis of Caffeine &amp; Benzoic Acid in Soft Drinks

The only thing I can think of is that it was in an aqueous solution (soda), so perhaps some benzoate will be in the form of benzoic acid and some will still be in the form of benzoate. By adding $\ce{HCl}$, we can force all the benzoate to be in the form of benzoic acid for better quantification.

Is this the correct line of thinking or am I missing something?
Your assumption is correct, the addition of HCl, as already in the earlier publication by McDevitt (J. Chem. Educ., 1998, 75, 625-629 DOI: 10.1021/ed075p625) ensures benzoates are converted into benzoic acids. 

The publication by Guo et al., is instructive as it lists several benzoic acids side by side, for example: 



source: J. Phys. Chem. A, 2012, 116, 11870–11879 DOI: 10.1021/jp3084293

The shift of the centre of absorption may be more important than a potential change in $\varepsilon$ if you want to use the UV-Vis spectrum recorded in a principal component analysis (PCA), where overlap of absorption bands of your consitiuents in the analyte should be avoided.