It depends on a number of factors, and some of the factors interact.
As far as using flash as the main source of illumination for a single-capture (i.e. non-stacked) image is concerned ...
To the extent that some of the following are the case, then natural light will often be preferable:
- The ambient light level is high
- The subject is relatively large*
- The subject is not moving
- You want or are happy with shallow depth of field
- Fine detail is not your primary concern
- You use a tripod or some other means of supporting the camera
- You prefer the look of natural light
- You don't like dark/black areas in backgrounds that flash can produce
- You don't like carrying around a flash and diffusion setup, and/or you don't like using the camera with such a setup
- You are ok carrying a tripod around
And to the extent that some of the following are the case, then flash will often be preferable
- The ambient light level is low
- The subject is small*
- The subject is moving
- You want large depth of field
- You want to see as much detail as possible in your images
- You work hand-held
- You have the flash well enough diffused to give sufficiently pleasing illumination
- You like or at least don't mind dark/black areas in backgrounds, or are prepared to use post processing to lighten them where possible
- You are ok with carrying around a flash and diffusion setup, and are ok using the camera with such a setup
- You don't like carrying a tripod around
* The size of the subject has to do with depth of field. As subjects get smaller you may need to use smaller apertures to get enough depth of field, and this may mean raising the ISO and/or slowing the shutter speed too much when using natural light.
When using strong natural light as the main source of illumination flash may be useful to soften harsh shadows or illuminate a subject which is in shadow, for example a flower with the light coming from behind it.
For example (and these are not recommendations, just an example of one particular way the many possibilities can play out).....
I work hand-held almost all the time.
I almost always use natural light as the main source of illumination for flowers and other botanical subjects, and only very, very rarely use fill flash. I like the look of natural light and the varied effects I can get with it. Ambient light levels can be quite low sometimes. This puts a premium on good image stabilisation, repeated captures to increase the chance of a sharp outcome and sometimes means stronger post processing is needed to cope with high ISOs.
I almost always use flash for insects, spiders and other invertebrates, the main exceptions being larger insects that I generally see in bright conditions (although not very often unfortunately), such as dragonflies and butterflies. Some of the invertebrates I photograph are quite small (down to 1 to 2 mm long) and some of them are moving around. I want large depth of field. I don't like very dark/black areas in backgrounds and I sometimes raise shadows a lot to reduce that effect, which means I may have to use strong noise reduction.
None of this is fixed. For example, until very recently I assumed that photographing water droplets on grass etc would need natural light because of getting horrible reflections of the flash heads/diffusers when using flash. The use of natural light would probably mean using a tripod. However, recently I discovered that I could get some nice results using flash, hand-held.
