Yes, there is a difference in pronunciation between 'elle aime' and 'elle n'aime'. If the 'n' is there, it is pronounced. 'Elle aime' is pronounced like 'Elemm' and 'Elle n'aime' is pronounced like 'Elnemm'.
That said, in relaxed conversation, French speakers often omit the 'ne' particle, and rely on the 'pas' to convey the negative meaning. In informal conversation, a French speaker will say 'Je l'aime pas' as opposed to the more strictly correct 'Je ne l'aime pas'. It isn't a case of pronunciation, though - the speaker is actually omitting the 'ne'. You will also see this form without the 'ne' written in informal contexts.