Please note your objection if you have indeed received the notice in hand after 30th September. Please note if speed post had come on 30th and you were not there or door was closed, it is a service on 30th even if you collect the speed post after a few days from the delivery office against intimation letter dropped by postman. service date of the notice would mean the 1st service by the postman even if your door is closed.
If the notice is served to you on or after 1st October, you are still duty bound to reply. If you or your CA cooperate with the department for the assessment, there is a new section 292BB from 1/4/2008 that suggests your cooperation will be deemed waiver of serving notice on time unless you record your objection before the completion of the assessment.
What I suggest (please take more opinions) is you record your objection to having been served the notice late if the postman's first attempt was on or after 1st October. After this the AO may serve notice under section 142(1) asking for details of loans and income sources etc.which you will have to comply with and furnish. Normally if the notice is served to you on time and there is no reply or cooperation from you the AO will complete the assessment u/s 144 using best judgement. Please remember that today AO is equipped with detailsof interest received by you without TDS also as well as your credit card expenses and payments (for salaried employee this is the problem when they use the credit card for employers expenses). He will use the best judgment option with all this information. I am unable to ascertain whether he can use best judgement if notice is served late. However, if you have the notice in hand late, I suggest you record your objection first and then give details for AO to complete assessment. If you cannot go yourself, please send someone with a letter of authority on stamp paper (non judicial and not court fee stamp) of denomination according to your state where you are assessed. In maharashtra (Mumbai, Pune, Nagpur etc. it is Rs.100). Do remember that AO is equipped with all your AIR information and what they are catching everyone on is the FDs where TDS is not done because of manipulations. The banks file the return and if by chance they have given your PAN even though no TDS is done, AO has the details in front of him. It is upto you to cooperate or not.