What are the effects of underwater "windmills"?
As you have noted, this technology is new, and so far only small numbers of experimental tidal energy converters (TECs) have been deployed. For this reason, little has been possible in the way of measurement, and so as you note, all estimates are based on models or other means of prediction.

To answer the second question first - how much the currents are affected depends how much of the energy you remove. Since the whole point of TECs is to remove energy from the flow, there must be some effect on currents. Garrett &amp; Cummins (2005) built a simple analytic model of a channel between two large basins (which reflects many tidal energy scenarios) and showed that if all other considerations (e.g. navigation, engineering practicality) are ignored then the maximum power that may be extracted from the channel is obtained when its flow rate is reduced by approximately two thirds. However, this scenario is unlikely to ever be obtained, and the real limit on energy extraction at a given site (if not an economic limit) will probably be determined by what level of environmental effects are deemed to be acceptable. The relationship between power extracted and effect on the flow is not a simple one, and in most cases a significant proportion of the available power could be obtained with a relatively small change to the local currents.

A number of modelling studies have been made of more realistic scenarios for early deployment (e.g. Admadien et al 2012). These typically predict local changes to current speeds of up to 30%, which fade after a few km. Typically there is a decrease in the flow speed in line with the TECs, and an increase to either side of the farm/array, as some of the flow diverts around the added impedence. Effects on residual velocity (i.e. that which is left in the long term when the tidal cycles are averaged out over a period of time), which is relevant to sediment transport processes, are predicted up to at least 15km away.

Some baroclinic modelling (Yang &amp; Wang 2013) has suggested increased mixing, and thus decreased stratification, as a result of the turbulence introduced by TECs. It is also conceivable that in other scenarios, stratification might be increased as a result of reduced flow speeds.

Physical effects, then, are likely to include direct effects on current speed, sediment, and stratification.

The obvious possible biological effect is from collisions. This is not my field, but as I understand it no effect is likely on small fish populations from collisions, although individuals may be affected. Collision risk for large animals (e.g. sharks and marine mammals)  and for diving birds is a topic of active research, and is likely (especially for mammals) to depend on their behaviour around the devices. No large animal collisions have been reported on any of the prototypes undergoing testing so far.

A good review of possible effects on benthic organisms is provided by Shields et al (2011). These may include,


Direct disruption of seabed habitats by physical interference, e.g. from moorings
Disruption of ecological niches: Some organisms have evolved to survive in areas where others cannot - e.g. high current speed environments. Changes in seabed conditions, e.g. from greater or lesser current speeds, may cause them to be out-competed by other species that can then settle there.
Similarly, changes to sediment distribution represent changes to seabed habitats.
Alteration of flow patterns could have implications for species with a dispersive juvenile stage (e.g. larvae that rely on currents to spread) or those that rely on current flow for nutrient or waste transport.