With logical encoding the search mechanism does not have to know anything about bi-directional text. Simply taking the search terms as typed and matching against the text will yield the correct results. With logical encoding one can use HTML efficiently as it was designed. Logically encoded pages may include nikud and ta'amei mikra. Visually encoded pages cannot.
Logical pages are cheaper to produce, simply since people always type Hebrew text logically.
Production of visually encoded pages must involve machine conversion from logical to visual. Putting them online will be cheaper and easier with logical encoding. Using efficient markup can make it easier to translate a website to another language, with minimal changes to markup. In some other scripts, such as the Arabic script, visual encoding is not an option, so one should expect increasing support for logical encoding. The advantages of the logical method as a long run solution are evident.