After some debugging, seems this is the cause:

diff --git a/src/interp/nruncomp.boot b/src/interp/nruncomp.boot
index 323080a1..cd7dbea6 100644
--- a/src/interp/nruncomp.boot
+++ b/src/interp/nruncomp.boot
@@ -137,7 +137,7 @@ optDeltaEntry(op,sig,dc,eltOrConst) ==
   sig := substitute(devaluate dcval, ndc, sig)
   if rest ndc then
      for new in rest devaluate dcval for old in rest ndc repeat
-       sig := substitute(new, old, sig)
+       sig := substitute(new, "$$", sig)
      -- optCallEval sends (List X) to (List (Integer)) etc,
      -- so we should make the same transformation
   fn := compiledLookup(op,sig,dcval)

So for

)abbrev domain TEST1 Test1
Test1 : with
   f1 : % -> Vector %
  == add
   f1 x == empty()

It used to generate

(SDEFUN |TEST1;f1;$V;1| ((|x| $) ($ |Vector| $)) (SPADCALL (QREFELT $ 7)))

After the patch, it generates:

(SDEFUN |TEST1;f1;$V;1| ((|x| $) ($ |Vector| $)) (MAKE-ARRAY 0))

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