When I select two searchable PDFs and combine them, I get a new document with just the text of both PDFs.
Can DT merge pdfs into a multiple page PDF? I know preview can, and PDFPen pro can (even has an applescript I read) but one more app in the process 
This script might be what you are looking for. It requires at least 10.4 OS.
Of course with dtpro 2.0 you can drag the thumbnails between documents. Try opening a separate window for the “source” document, selecting the thumbnails, and dragging them into the thumbnail area of the target document. It’s a bit buggy still, but it works!
I use the script when I’ve got heavier duty merges to do…
-erico
--merge selected pdfs with leopard's python merge utility
--by eric oberle v1.1
property temp_directory : "/tmp/devonthink/combine-pdfs"
property export_path_posix : temp_directory & "ocr/"
property export_path_nonposix : (POSIX file export_path_posix)
tell application "DEVONthink Pro"
set cupos to selection of window 1
set reimport_location to current group
try
if reimport_location is {} then set reimport_location to {}
on error
set reimport_location to {}
end try
end tell
---main loop
try
do shell script ("mkdir " & temp_directory & ";rm -r " & temp_directory & "/*")
end try
tell application "DEVONthink Pro"
set this_record to first item in cupos
set the_name to (the name of this_record)
if the_name does not end with ".pdf" then
set the_name to the_name & "-complete.pdf"
end if
set the_comment to comment of this_record
set the_kind to kind of this_record
set the_url to URL of this_record
repeat with this_item in cupos
if the name of this_item does not end with ".pdf" then
set the name of this_item to ((the name of this_item) & ".pdf")
set the_comment to the_comment & return & comment of this_item
end if
my export_pdf(this_item, temp_directory)
end repeat
set merge_pdf_command to "python '/System/Library/Automator/Combine PDF Pages.action/Contents/Resources/join.py' -o '" & temp_directory & "/joined.pdf' " & temp_directory & "/*.pdf"
do shell script (merge_pdf_command)
set merged_pdf to import (temp_directory & "/joined.pdf") to reimport_location
set comment of merged_pdf to the_comment
set URL of merged_pdf to the_url
end tell
on export_pdf(the_record, temp_directory)
---returns finder-path of exported file
tell application "DEVONthink Pro"
if the parent of the_record is not {} then
set reimport_location to the first item of the parent of the_record
else
set reimport_location to root of current database
end if
set exported_file_with_path to export record the_record to temp_directory
log "exported_fwp " & exported_file_with_path
end tell
return {exported_file:exported_file_with_path, reimport_loc:reimport_location}
end export_pdf