You can change those limits; but you'll be using some time in the data transfer between the DB and the client, and possibly for the display; and that in turn would be affected by the number of rows pulled by each fetch. Those things affect your application as well though, so looking at the raw execution time might not tell you the whole story anyway.
To change the worksheet (F5) limit, go to Tools->Preferences->Database->Worksheet, and increase the 'Max rows to print in a script' value (and maybe 'Max lines in Script output'). To change the fetch size go to the Database->Advanced panel in the preferences; maybe to match your application's value.
This isn't perfect but if you don't want to see the actual data, just get the time it takes to run in the DB, you can wrap the query to get a single row:
select count(*) from (
<your original query
);
It will normally execute the entire original query and then count the results, which won't add anything significant to the time. (It's feasible it might rewrite the query internally I suppose, but I think that's unlikely, and you could use hints to avoid it if needed).