I'd create two different css classes in this case.
Here you'll find how to include css files (as many as you like) into a shiny app.
To switch between the classes we can use addCssClass/ removeCssClass (or toggleCssClass) from library(shinyjs):
library(shiny)
library(shinyjs)
if(!dir.exists("www")){
dir.create("www")
}
writeLines(".dark {
background-color: black;
color: white; /* text color */
}", con = "www/dark_mode.css")
writeLines(".light {
background-color: white;
color: black; /* text color */
}", con = "www/light_mode.css")
ui <- fluidPage(
useShinyjs(),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "dark_mode.css"),
tags$link(rel = "stylesheet", type = "text/css", href = "light_mode.css")
),
radioButtons("mode", "Select mode", choices = c("dark", "light"), selected = "light")
)
server <- function(input, output, session) {
observeEvent(input$mode, {
if(input$mode == "dark"){
addCssClass(class = "dark", selector = "body")
removeCssClass(class = "light", selector = "body")
} else {
addCssClass(class = "light", selector = "body")
removeCssClass(class = "dark", selector = "body")
}
})
}
shinyApp(ui, server)

The same can be done via Shiny.addCustomMessageHandler and some custom JS using e.g. element.classList.add("myclass"); (see this).
Edit: Apply addCssClass to inputs of different classes:
library(shiny)
library(shinyjs)
if(!dir.exists("www")){
dir.create("www")
}
writeLines(".dark {
background-color: black !important;
color: white; /* text color */
}", con = "www/dark_mode.css")
writeLines(".light {
background-color: white !important;
color: black; /* text color */
}", con = "www/light_mode.css")
ui <- fluidPage(
useShinyjs(),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "dark_mode.css"),
tags$link(rel = "stylesheet", type = "text/css", href = "light_mode.css")
),
radioButtons("mode", "Select mode", choices = c("dark", "light"), selected = "light"),
selectizeInput("Test", "Test Input", choices = 1:10),
actionButton("testButton", "Test Button")
)
server <- function(input, output, session) {
observeEvent(input$mode, {
applyTo <- list(".selectize-input", ".btn-default")
if(input$mode == "dark"){
lapply(applyTo, function(x){
addCssClass(class = "dark", selector = x)
removeCssClass(class = "light", selector = x)
})
} else {
lapply(applyTo, function(x){
addCssClass(class = "light", selector = x)
removeCssClass(class = "dark", selector = x)
})
}
})
}
shinyApp(ui, server)

Edit: using forEach:
library(shiny)
library(shinyjs)
if(!dir.exists("www")){
dir.create("www")
}
writeLines(".dark {
background-color: black !important;
color: white; /* text color */
}", con = "www/dark_mode.css")
writeLines(".light {
background-color: white !important;
color: black; /* text color */
}", con = "www/light_mode.css")
ui <- fluidPage(
useShinyjs(),
tags$head(
tags$link(rel = "stylesheet", type = "text/css", href = "dark_mode.css"),
tags$link(rel = "stylesheet", type = "text/css", href = "light_mode.css")
),
radioButtons("mode", "Select mode", choices = c("dark", "light"), selected = "light"),
selectizeInput("Test", "Test Input", choices = 1:10),
actionButton("testButton", "Test Button")
)
server <- function(input, output, session) {
dm_classes <- paste(c(".selectize-input", ".btn-default"), collapse = ", ")
observeEvent(input$mode, {
if(input$mode == "dark"){
runjs(sprintf("document.querySelectorAll('%s').forEach(x=>x.classList.add('dark'));
document.querySelectorAll('%s').forEach(x=>x.classList.remove('light'));", dm_classes, dm_classes))
} else {
runjs(sprintf("document.querySelectorAll('%s').forEach(x=>x.classList.add('light'));
document.querySelectorAll('%s').forEach(x=>x.classList.remove('dark'));", dm_classes, dm_classes))
}
})
}
shinyApp(ui, server)