This answer is primarily based on Ignace Feuerlicht, "Omissions and Contradictions in Kafka's Trial", The German Quarterly 1967, 40(3), pp. 339-350 - available here if you have Jstor access. All quotes below are from this article.
Josef K.'s last name is not the only, though perhaps it is the most prominent, piece of information which is carefully not stated in The Trial. The setting of the novel is also omitted, as are the names of several other characters, and of course the nature of Josef K.'s crime. So it could be said that secretiveness and omission are themes in The Trial as a whole.
Focusing now on the main question, there are a few possible interpretations. (Quotes below are all from the Feuerlicht article.)
Symbolising his emptiness and lifelessness.
This theory seems convincing at first glance, but it doesn't hold much water when we compare Josef K. to other characters in the book with or without their surnames specified:
The lack of his
last name can be taken and has been taken as a sign and accusation
of his emptiness, lifelessness, or of the anonymity and fragmentation
of modern life, especially that of the middle class. But Rabensteiner
or Miss Montag, for instance, are not more alive or greater individ-
ualists than K., in spite of their full last names. Another "accused"
man is actually the only one in the novel to have a first and a last
name (Rudolf Block). K.'s antagonist, the assistant director, has
no name at all; nor are the names of the director, the priest, or
any high Court official, or the Court itself mentioned.
Indicating Kafka's contempt for him.
There is some evidence for this theory in the words of Kafka himself:
In
a diary entry of a day when he might have been working on the
Trial (27 May, 1914), Kafka writes that he finds the "K" ugly,
almost nauseating. "And yet I write it down, it must be characteristic
of me" (T, 375).1 To be sure, the passage refers only to the letter
"K" as written by Kafka, and not to any symbolic or philosophic
meaning which it might have for Kafka or for his novel.
Denoting Franz Kafka himself.
In German, the letter K is called "ka", so Kafka sounds almost like K-fK. And the final letter of "Josef" gives us the F, so "Josef K." almost rhymes with "Kafka".
K., to be sure, is in some respects akin
to Kafka. He is employed by a large firm, is single, and has a decisive
experience at the age of thirty (Kafka had a literary breakthrough
when he wrote "Das Urteil" at about that age). But he is in many
ways Kafka's opposite. Unlike Kafka, he does not suffer from a
"father complex" or from an "infinite" guilt (H, 196), but is full
of self-confidence. He does not seem to possess any creative abilities.
He is a self-made man and quite satisfied with his job. While K. probably is of average height (he is shorter than Willem
and taller than Block), Kafka was six foot tall. Unlike K., Kafka
frequently suffered from insomnia and headaches, often was late
for appointments, did not wear heavy clothing in winter, and did
not drink any liquor.
Denoting Franz Kafka's father Herrmann.
Perhaps this other Kafka would be a better analogy for the role - the surname connection doesn't necessarily imply a representation of the author himself.
[L]ike
K., Kafka's father was a self-made man, had an oratorical flair,
looked down on people below his social rank, was of robust health,
had frequent fits of anger, and was superficially religious. He, too,
had an experience at the age of thirty that started a new chapter
in his life: He opened a store in Prague. And, for the benefit of those
who believe that "the man from the country" in the Türhüterlegende
corresponds to K., Kafka's father was literally a man from the
country. But in spite of the similarities and in spite of the initial
"K," Josef K. is neither a dehydrated Franz Kafka nor an emasculated
Herrmann Kafka, but a literary figure in his own rights and with
his own life.
So there you go. Four different theories for why Josef K.'s last name was never revealed, each with reasons both for and against believing it. Take your pick.
1 Cited to Franz Kafka, Der Prozeß
(Berlin, 1951). H stands for Hochzeitsvorbereitungen auf dem
Lande (New York, 1953) and T for Tagebucher (New York, 1948).