I'm interested to know when the actual phrase smile one's thanks was first registered in the English language, as well as smile agreement and nod agreement.
OED gives three citations from Shakespeare for smile as a transitive verb...
1598 Love's Labour's Lost v. ii.
Some Dick That smyles, his cheeke in yeeres.
1609 Pericles xxi. 127
Thou doest looke like patience..smiling extremitie out of act.
1616 Twelfth Night (1623) iii. ii.
He does smile his face into more lynes, then is in the new Mappe.
OED's first citation for transitive nod is a 1522 translation of Virgil's Æneid, but it's not until over a century later that we see it used with anything other than head[s] as the object (1667, in Dryden's Annus Mirabilis - "He..nods at every house his threatning fire.").
OP's specific pairings smile thanks and nod agreement are trivial variants once the possibility of transitive usage is established within the language.
In 'An historical syntax of the English language' [Vol 1 part 3] by F T Visser, a section dealing with these 'pseudo-report' verbs (and novel quotative verbs) is found:
Transitivisation may also have been furthered by the fashion which set in in later modern English – especially in novels – of treating verbs expressing human and animal sounds (such as bellow, coo and groan) as well as verbs such as smirk, smile and persist as if they were synonyms of say by giving them the quoted words as object [ie using novel quotative verbs].
She smiled “I don’t believe you”
He grunted “I thank you”
She smiled disbelief
He grunted his gratitude
[so novel quasi-report structures] was only a step. [tidied]