There is very little difference. To test this I created a new directory with a file "bug3.odt".
I then created two links to it using the command line
ln -s bug3.odt bug_ln and
ln -s /home/warren/qaz/bug3.odt bug_ln2 then finally went into nautilus and created a link by right clicking on the file and selecting "Make Link".
The result was as follows
warren@dell:~/qaz$ ls -la
drwxrwxr-x 2 warren warren 4096 Feb 18 20:14 .
drwxr-xr-x 69 warren warren 12288 Feb 18 20:11 ..
-rw-rw-r-- 1 warren warren 18505 Nov 12 20:11 bug3.odt
lrwxrwxrwx 1 warren warren 8 Feb 18 20:12 bug_ln -> bug3.odt
lrwxrwxrwx 1 warren warren 25 Feb 18 20:14 bug_ln2 -> /home/warren/qaz/bug3.odt
lrwxrwxrwx 1 warren warren 25 Feb 18 20:13 Link to bug3.odt -> /home/warren/qaz/bug3.odt
As you can see both
Link to bug3.odt have the same owner, group, permissions and link to the same location. Right clicking in nautilus is equivalent to using ln -s with the full path to the file.
It is also possible to create a link by holding down CTRL+SHIFT and dragging the file. This works in exactly the same way: equivalent to using ln -s with the full path to the file.