Did anyone use D2PAK and DPAK high power diodes with surface mount heat sinks from Aavid or Future electronics? If so would you please share your experience.

With the heat sinks mounted directly on the board and connected electrically, do they create any EMI issue?
If the power dissipation is high like 40 to 50 W, then what is the better way of cooling? - the bottom cooling using thermal vias and additional heat sink or the top cooling with standard surface mount heat sinks.

A worst case thermal analysis is a must in order to keep the junction at a reasonable temperature. Every layout is unique and all power devices have to be taken into the whole picture. Thermal via's are only effective when situated directly under the device and filled with thermally conductive medium.
40 to 50 W dissipation on a single D2PAK device?

There may be some standard way of cooling these devices (D2PAK and DPAK), because many manufacturers have their standard product variants in these packages. For example, the ST Microelectronics 950V, 17A MOSFET STB20N95K5 in D2PAK and Cree's 1200V, 14A diode C4D10120E-ND in D2PAK are high power devices. So what would be the design of heat sinks for these devices to be used.
The surface mount heat sinks from Aavid has a thermal resistance of 3 to 4 C/W at 300 LFM.
Other people have used thermal vias on PCB and bottom cooling with heat sinks. But are there any standard ways to cool these packages.

There is no standard as every design/layout is unique as well as the ambient conditions. Another thing to consider is that many of the device specifications are misleading as to maximum operating parameters are based on a junction of 25 deg C. The actual operating conditions as to voltage/current has to be taken into account and then the thermal resistance of the device. Then the thermal analysis can start.

First of all, as best as I know, there is no "standard" way of mounting these things.

I've seen the Aavid SM heatsinks attached to the devices per the manufacturer's soldering recommendations and placed in the air stream of an appropriate fan with effective results.

EMI will, of course, be related to the node to which the heatsink is soldered. You'll have to figure that one out for your self and make sure that it's quiet.

One technique I've used successfully is to mount the D2PAK's or DPAK's on the bottom of the pc board. The board is then "pressed" against a heatsink that runs along the bottom of the board. To improve the compliance of the mounting surface, I've used some relatively thick and "spongy" thermal material, such as Bergquist's "Gap Pad", between the device(s) and the heatsink. You can buy similar thermal material from the usual suspects, and it can be purchased with adhesive backing. This allows you to use a minimum amount of material, which can then be located accurately on the 'sink.

Admittedly, the plastic package doesn't have the greatest thermal resistance, but this technique significantly improves thermal performance.