Yes, this will effect your application. Your application will be refused straightaway.
Your time for conditional discharge has passed, but it does not change the fact that you were convicted of an offence. According to current laws, the record of conviction will remain in the Police National Computer until you are 100 years old.
This does not at all mean that you will not qualify for naturalisation until you are 100 years old.
Home office's current criteria for non-custodial sentences (including conditional discharge) is that a person must wait 3 years from date of conviction before they can pass the good character requirement.
So, you must wait until full three years have passed from the date of conviction. After 3 years have passed, and when you apply for naturalisation, you must still disclose your conviction, but home office will disregard this conviction.
Once again, please note that even though after 3 years from date of conviction, the conviction will be disregarded, you must still disclose it on application form. If you fail to disclose, UKBA will refuse your application for non-disclosure.
Also keep in mind that any repeat of this offence, or some other offences might result in your application being refused for a much longer period than 3 years.
regards