Some functions which take xtable objects and print as kable objects, keeping track, extracting the caption automatically, and then using pandoc-tablenos for referencing.

xtable2kable.R

assignCount <- function(obj, kind, new=FALSE) {
    # fromi https://rmflight.github.io/posts/2012/10/papersinRmd.html
    incCount <- function(inObj, useName) {
        nObj <- length(inObj)
        useNum <- max(inObj) + 1
        inObj <- c(inObj, useNum)
        names(inObj)[nObj + 1] <- useName
        inObj
    }

    kindCount <- paste0(kind, 'Count') # create counting object ('tblCount' or 'figCount')
    kind1 <- paste0(kind,'1') # initializing value ('tbl1' or 'fig1')
    if(!exists(kindCount) | new) {
        kind0 <- 1 # create first value of counter
        names(kind0) <- kind1 # assign correct kind name
        assign(kindCount, kind0, envir = .GlobalEnv) # create counter if doesn't exists
        assign(kind1, obj, envir = .GlobalEnv) # add first table
        rm('kind0')
    } else {
        kindNext <- paste0(kind, length(get(kindCount)) + 1)
        assign(kindNext, obj, envir = .GlobalEnv)
        assign(kindCount, incCount(get(kindCount), kindNext), envir = .GlobalEnv) # update counter
    }
}

## tabular2xtable
tabular2xtable <- function(x, caption=NULL){
    cat("\\begin{table}[ht]\n")
    cat("\\centering\n")
    latex(x)
    if(!is.null(caption)) cat("\\caption{",caption,"}\n", sep="")
    cat("\\end{table}\n")
}

## Print Table
printTable <- function(tbl, label=NULL, new=FALSE) {
    stopifnot(!is.null(label))
    if(!is.null(label)) stopifnot(inherits(label, 'character'))
    assignCount(tbl, kind='table', new=new)
    num <- length(tableCount)
    tableCount[num] <- label
    cap <- paste0(attr(tbl, "caption"), " {#tbl:", label,"}")
    kable(tbl, caption=cap)
}

## reference Table
refTable <- function(label) {
    I(paste0("@tbl:", label))
}

## Print Fig
printFig <- function(fig, label=NULL, new=FALSE) {
    stopifnot(!is.null(label))
    if(!is.null(label)) stopifnot(inherits(label, 'character'))
    assignCount(fig, kind='table', new=new)
    num <- length(tableCount)
    tableCount[num] <- label
    cap <- paste0(attr(fig, "caption"), " {#fig:", label,"}")
    kable(fig, caption=cap)
}

## reference Fig
refFig <- function(label) {
    I(paste0("@fig:", label))
}