2. The choice is either "fastest possible" or "I just don't care how long it takes" - for either development or run time. There is usually no middle ground.
3. Tooling - the scientist is most likely using a text editor not an IDE (especially when they start working). Fortran and python are both low enough on boilerplate to not need IDE support.
4. Abstraction level. Scientists in general don't bother care about abstraction level at all. Procedural programing's abstractions are usually more than enough for them (and may actually be the correct level for some numerical work - think cache misses vs. hits).
5. Some areas of science do use Java (check out imagej for example).