I spent many years using GUI tools for SQL in various platforms. But the tool will always choose a pre-defined structure given a pre-defined input.
When I was forced to write with no tool in order to use the most current features, I discovered SQL is much more powerful than any tool can implement. To me GUI tools mean not having to think, to just settle for "good enough". Tools may increase volume of code, I doubt they increase quality of code.

The question has 2 parts:

- querying an Oracle database
The tool that executes the query is not important, it will only make it easier to view and export the results. More important: don't trust generated queries. Query-builders like the one included in SQL Developer can assist an unexperienced user, but they are dumb and usually produce less than optimal SQL. So in this case it would be the ease of handling or the license fees as a factor. I worked a lot with Toad, but I think it is a little bloated. At the moment I use SQL Developer for queries amongst other things because of the easy to use reporting feature for recurring executions.

- carrying out updates
I would always use a script that runs in SQL*PLUS. This is the only way to ensure that changes can be propagated from development to test and production in a reproducible way.

The best tool is our ability to learn and understand the systems we are working with which allows us the ability to adapt to change.

Whenever I go to a site which I don't know, I am happy to have sqlplus always on my side as "a friendly interactive editor" (afiedt.buf). For sites which I have some control on, I am using a free product from my company ( http://www.invantive.com/products/invantives-free-query-tool/ ). It is more GUI and also supports SQL Server and others, since my isql knowledge is a lot worse than sqlplus.