Daijr and koj actually have separate ようど/沃度 and ヨード/沃度 entries but I think it's OK to ignore the hiragana reading. Daijs and meikyo only have katakana (and the 沃度 ateji).

@@ -15,0 +16,4 @@
+<r_ele>
+<reb>ようど</reb>
+<re_inf>&sk;</re_inf>
+</r_ele>
@@ -18 +22 @@
-<xref type="see" seq="1547420">沃素</xref>
+<xref type="see" seq="1547420">ヨウ素</xref>

I think this is our usual style with loanwords that have ateji

Google N-gram Corpus Counts
╭─ーーーー─┬───────┬───────╮
│ ヨードが │ 4,865 │ 93.2% │
│ 沃度が　 │     0 │  0.0% │
│ ようどが │   185 │  3.5% │
│ ヨウドが │   171 │  3.3% │
├─ーーーー─┼───────┼───────┤
│ ヨードを │ 5,799 │ 93.2% │
│ 沃度を　 │    32 │  0.5% │
│ ようどを │    54 │  0.9% │
│ ヨウドを │   336 │  5.4% │
╰─ーーーー─┴───────┴───────╯

@@ -10 +10 @@
-<reb>ようど</reb>
+<reb>ヨード</reb>
@@ -13,2 +13,2 @@
-<reb>ヨード</reb>
-<re_nokanji/>
+<reb>ヨウド</reb>
+<re_inf>&sk;</re_inf>

Koj: ヨード【Jod ドイツ・沃度】
Daijr: よう-ど エウ― [1] 【沃度】 ⇒ヨード
沃度	3766	3.4%
ようど	2843	2.6%
ヨード	104494	94.1%

@@ -6,0 +7 @@
+<ke_inf>&rK;</ke_inf>
@@ -18,0 +20 @@
+<misc>&uk;</misc>
@@ -20 +22 @@
-<gloss>iodine</gloss>
+<gloss>iodine (I)</gloss>

沃度	3766	1.7%
沃素	3283	1.4%
ヨウ素	109752	48.2%
よう素	6176	2.7%
ヨード	104494	45.9%

As already noted, from German Jod.  Minimally, the　度　doesn't seem to actually mean anything.  Not sure what an authoritative source would be on that, but google of 沃度　当て字 will turn up results.

Here's one:
http://s.jlogos.com/d001/705426670.html
沃素(ようそ)。▽「沃度」は当て字。(ドイツ)Ｊｏｄ

Interestingly, ヨウ素 and ヨード seem to be almost equal in popularity, both in kana and kanji forms.

@@ -5,0 +6 @@
+<ke_inf>&ateji;</ke_inf>