Is there a way ,or some steps which ensure any custom module/code written in Magento is adhering to all standard/best practices, without it breaking Magento in any case i.e upgrades,extension conflicts etc.
As others already pointed out, the best way is of course to let an experienced Magento developer manually review the code. He does not necessarily need to be a certified developer, but he should of course be experience in Magento and should know the best practices.
Anyway, if you would like to do an automatic check of extension, have a look at the following resources:
The first thing you should do is doing a diff between the codebase you have and the official version of Magento, in the app/code/core folder. With that you might be able to tell if the core files have been modified.
Inchoo has a great guide for that here. In the case of custom modules there is not much to do but to check them one by one and enabling/disabling them to see which one is causing conflicts.
There are some interesting guides in the wild too, just search "check magento conflicts" in Google or here and you will see a few guides from the big players. One of my favourites is this guide from Ashley Schroder.
You don't need a certified developer, it does allow your senior manager to sleep better at night, but doesn't actually mean they know any more - sometimes the opposite. The key to good code is combining business processes and technical code, however that is quite rare. Every problem can be fixed with business processes -or- technical code - combining the two is the most optimal as it leads to 10s to 100s lines of code rather than 1,000s and 10s of extensions.
So the best practice, have as little code as possible written to solve the problem and use as few extensions as possible. The more code there is the more problems you are likely to have.
The problem with Magento is that its natural habitat is Micro and Small Enterprise (sub $3mil & sub $14mil/yr revenue companies). Due to this most of the development resource will try and code their way out of the problem - this destabilises the platform. It is also part of the reason you will not find a 'best practice' for Magento like you do for solutions such as SAP (the consultants we work with have both Magento & SAP experience) - they created their own.
Unfortunately 99.9% of Magento resource would not understand these 'best practices' as it goes against the platforms natural level - the best practice is to keep it as simple as possible - the problem is that the community are averse to such 'practices'. This would mean very few extensions, very little custom code, and try not to push the plaform to do something it is not naturally designed to do - it is not Hybris or ATG.