Following convention helps scanning

Users would have visited a lot of websites by the time they get to yours, and following the existing conventions will give the sense of familiarity to your users. This familiarity is important as it will allow users to scan your web pages, deciding what they could click and what they could ignore very quickly (Websites should be designed for scanning).

For example, most users will have the preconceived ideas of how buttons would look like, so ensuring that buttons look clickable will give users familiarity. Designing links that look clickable will have the same effect. Navigation bar is most commonly located on the top, and the same to websites logo as well.

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References

Krug, Don’t make me think (p. 31).

When applied well, Web conventions make life easier for users because they don't have to constantly figure out what things are and how they're supposed to work as they go from site to site.

Krug, Don’t make me think (p. 101).

As we scan a page, we're looking for variety of visual cues that identify things as clickable (or "tappable" on touch screens) - things like shape (buttons, tabs, etc.), location (in a menu bar, for instance), and formatting (colour and underlining).