- Spaces after the comma in the optional argument of
\author are not supported by class elsarticle. ☹
- Also the class does not generate a rerun warning, the letters for the affiliations are not yet known in the first LaTeX run.
A. Example without merging
\documentclass[authoryear]{elsarticle}
\begin{document}
\begin{frontmatter}
\title{A Very Clever Paper Title}
\author[add1]{Author1}
\ead{email1@domain.ca}
\author[add2,add3]{Author2}
\ead{email2@domain.ca}
\author[add2,add3]{Author3}
\ead{email3@domain.ca}
\address[add1]{Department of Redundancy Department}
\address[add2]{Centre for Study of Things}
\address[add3]{Department of Interests}
\end{frontmatter}
\end{document}

B. Two affiliations in one line
\author[add1]{Author1}
\ead{email1@domain.ca}
\author[add2]{Author2}
\ead{email2@domain.ca}
\author[add2]{Author3}
\ead{email3@domain.ca}
\address[add1]{Department of Redundancy Department}
\address[add2]{Centre for Study of Things; Department of Interests}

- Disadvantage: The second affiliation in the line gets lost visually.
It is not clear, that the both authors have two affiliations.
C. Affiliations in two lines
\author[add1]{Author1}
\ead{email1@domain.ca}
\author[add2]{Author2}
\ead{email2@domain.ca}
\author[add2]{Author3}
\ead{email3@domain.ca}
\address[add1]{Department of Redundancy Department}
\address[add2]{%
\begin{tabular}[t]{@{}l@{}}
Centre for Study of Things\\
Department of Interests
\end{tabular}%
}

- Disadvantage: IMHO better than the previous variant, but it is not clear at the first glance that there are two affiliations under "b" and that both authors have two affiliations.
Summary: I prefer the first version A, clear and simple.