Both styles are used within the Go's standard libraries.
if len(s) > 0 { ... }
can be found in the strconv package: http://golang.org/src/pkg/strconv/atoi.go
if s != "" { ... }
can be found in the encoding/json package: http://golang.org/src/pkg/encoding/json/encode.go
Both are idiomatic and are clear enough. It is more a matter of personal taste and about clarity.
Russ Cox writes in a golang-nuts thread:
The one that makes the code clear.
If I'm about to look at element x I typically write
len(s) > x, even for x == 0, but if I care about
"is it this specific string" I tend to write s == "".It's reasonable to assume that a mature compiler will compile
len(s) == 0 and s == "" into the same, efficient code.
...Make the code clear.
As pointed out in Timmmm's answer, the Go compiler does generate identical code in both cases.