Cratchit does not want to anger Scrooge, of course. Scrooge would disapprove of him listening in and especially of him agreeing with Fred. "Involuntary" means that he was so moved and overcome with emotion from Fred's speech that he found himself clapping. Scrooge threatens to let him celebrate Christmas by losing his job.
Note the word "involuntarily." This indicates the way that the clerk, Bob Cratchit, applauded automatically in whole-hearted agreement without thinking of the reaction or the wrath that he might bring down upon himself from Scrooge. This in turn reinforces the profoundly bizarre and unnatural feelings that Scrooge has about Christmas. The words of the nephew tap in to some deep essential nature about the goodness of humanity and the way this is expressed at Christmas, which in turn makes Cratchit applaud loudly.
I take that quote to mean that the clerk, Bob Cratchit, suddenly applauded the words of Scrooge's nephew, who was praising Christmas to his nasty-tempered uncle. Bob was so pleased with what Fred said that he just suddenly clapped out loud without even thinking about what Scrooge might think of him for doing so:
"'But I am sure I have always thought of Christmas time, when it has come round - apart from the veneration due to its sacred name and origin, if anything belonging to it can be apart from that - as a good time: a kind, forgiving, charitable, pleasant time: the only time I know of, in the long calendar of the year, when men and women seem by one consent to open their shut-up hearts freely, and to think of people below them as if they really were fellow-passengers to the grave, and not another race of creatures bound on other journeys. And therefore, uncle, though it has never put a scrap of gold or silver in my pocket, I believe that it has done me good, and will do me good; and I say, God bless it!'
The clerk in the tank involuntarily applauded: becoming immediately sensible of the impropriety, he poked the fire, and extinguished the last frail spark for ever."
It means the clerk applauded but didn't want to because he was afraid of what Scrooge might think. The 'tank' refers to the little cell or room that the clerk is sitting in. This comes from Stave 1, Marley's Ghost