The dictionary.reference.com link that you gave shows only one sense for acquiesce: "to assent tacitly; submit or comply silently or without protest; agree; consent: [eg] to acquiesce halfheartedly in a business plan", from which one might (but shouldn't) suppose acquiescence is necessarily silent. However, other dictionaries, with senses like "To concur upon conviction; as, to acquiesce in an opinion; to assent to; usually, to concur, not heartily but so far as to forbear opposition" make it more clear that acquiescence need not be silent, merely not hearty.
This is made more explicit in wiktionary:
- (intransitive) To rest satisfied, or apparently satisfied, or to rest without opposition and discontent (usually implying previous opposition or discontent); to accept or consent by silence or by omitting to object; — followed by "in", formerly also by "with" and "to".
- (intransitive) To concur upon conviction; as, to acquiesce in an opinion; to assent to; usually, to concur, not heartily but so far as to forbear opposition.
Edit: Former protest or reservations may be implied when acquiescence is done unhappily or reluctantly; I think it is not implied in other cases. For example:
They frowned and grumbled and slowly acquiesced. – Implies some protest
They acquiesced and turned away. – One cannot tell about protest
They smiled and grinned and eagerly acquiesced. – Implies no protest; but is unusual usage