Overall, this question is rather broad, and will likely have an issue with opinions obscuring facts, so I'll try to keep this answer purely-factual.
say e.g. am using aircrack in windows what will be my disadvantage ?
We can answer that right from the developers of Aircrack:
This tutorial is focused on linux. Yes, I realize that linux is a problem for many people. Unfortunately Microsoft Windows simply does a poor job supporting the aircrack-ng suite. This is primarily due to the proprietary nature of the operating system and wireless card drivers. See Tutorial: Aircrack-ng Suite under Windows for Dummies for more details. Bottom line, don't use the aircrack-ng suite under Windows. There is little or no support for it.
First and foremost, Windows is virtually useless for wireless activities due to the huge number of restrictions. The restrictions do not come from the aircrack-ng suite so please don't ask for enhancements.
Here is a quick recap of the limitations:
Very few supported wireless cards: There are very few wireless cards which will work with the aircrack-ng suite. Most laptops come with Intel-based cards and none of these are supported. See the following links: Compatibility, Drivers, Which Card to Purchase and Tutorial: Is My Wireless Card Compatible? for more information. It is also important to note that there is little or no documentation accurately describing which version of the third party drivers you require for each card.
Dependency on third parties: The Windows world is highly proprietary and thus the source code for the drivers is not available publicly. As a result, no troubleshooting or fixes are available from the aircrack-ng team for these third party drivers. If there is a problem, you are on your own.
Limited operating system support: The Windows version works best with WinXP. It does not support Win98, some people have reported success with Win2000 but many have been unsuccessful with it and Vista is not supported. There is some evidence that a few people have aircrack-ng working under Vista but most people report failures. So basically, your best chance of success is under WinXP.
Passive capture of packets: Most people want to test the WEP security on their own access point. In order to do this, you must capture in the order of 250,000 to 2,000,000 WEP data packets. This is a lot of packets. With Windows, you can only capture packets passively. Meaning, you just sit back and wait for the packets to arrive. There is no way to speed things up like in the linux version. In the end, it could take you days, weeks, months or forever to capture sufficient packets to crack a WEP key.
Limited GUI: Most of the aircrack-ng suite tools are oriented towards command line utilization. There is only a very limited GUI available to assist you. So you must be more technically literate to successfully use these tools. Thus, if you are used to running a Windows installer then clicking your way to happiness, you are going to be exceedingly unhappy and lost with aircrack-ng.
Technical Orientation: Dealing with wireless requires a fair amount of operating system, basic wireless and networking knowledge. If you don't have this or are not prepared to do your own research, then you will find the tools and techniques bewildering. Do not expect people on the forums or IRC to answer basic knowledge questions. It is up to you to have these skills before starting out.
If you truly want to explore the world of wireless then you need to make the commitment to learn and use linux plus the aircrack-ng suite linux version. An easy way to start is to utilize the Backtrack live distribution. This distribution has the aircrack-ng suite plus patched drivers already installed which jumpstarts your learning process. BackTrack information can be found here.
So as a quick overview, the developers of Aircrack state that support for Windows is very limited, not because they haven't developed full support, but because the platform itself limits what they can do.