If it's 50-50 I'd prefer to stick with what's in most references.

@@ -11 +11,2 @@
-<reb>なみせん</reb>
+<reb>はせん</reb>
+<re_restr>波線</re_restr>
@@ -14,2 +15 @@
-<reb>はせん</reb>
-<re_restr>波線</re_restr>
+<reb>なみせん</reb>

sankoku redirects to "なみせん"
daijr/s, meikyo, obunsha, nikk all use "なみ線"/なみせん in the definitions
the majority of youglish results (excluding videos of the same channel/unclear audio) use "なみせん", though it's arguably still close to 50-50

my guess is that most people just use "なみせん" and "はせん" has a more "technical language" vibe

@@ -10,0 +11,3 @@
+<reb>なみせん</reb>
+</r_ele>
+<r_ele>
@@ -13,3 +15,0 @@
-</r_ele>
-<r_ele>
-<reb>なみせん</reb>

Youglish search results for "波線" are mixed between はせん and なみせん. Hard to say which one is more popular.

Google N-gram Corpus Counts
╭─ーーーー─┬───────┬───────╮
│ 　波線が │ 3,540 │ 90.3% │
│ なみ線が │   380 │  9.7% │
├─ーーーー─┼───────┼───────┤
│ 　波線の │ 2,446 │ 32.0% │
│ なみ線の │ 5,209 │ 68.0% │
├─ーーーー─┼───────┼───────┤
│ 　波線を │ 2,869 │ 87.1% │
│ なみ線を │   424 │ 12.9% │
├─ーーーー─┼───────┼───────┤
│ 　波線は │ 1,470 │ 70.7% │
│ なみ線は │   609 │ 29.3% │
├─ーーーー─┼───────┼───────┤
│ 　波線に │ 1,147 │ 46.5% │
│ なみ線に │ 1,320 │ 53.5% │
╰─ーーーー─┴───────┴───────╯

Adding "なみ線"

@@ -6,0 +7,3 @@
+<k_ele>
+<keb>なみ線</keb>
+</k_ele>
@@ -8,0 +12 @@
+<re_restr>波線</re_restr>

kojien, daijirin, daijisen, prog waei, gg5, shinmeikai, meikyo

all these dictionaries have this as はせん.  only shinmeikai also has なみせん as a full entry

@@ -6,0 +7,3 @@
+<r_ele>
+<reb>はせん</reb>
+</r_ele>

http://ja.m.wikipedia.org/wiki/波ダッシュ

My Japanese girlfriend referred to it as namisen and when I told her in the dictiionary it's reda as hasen she told me it's wrong and referred me to that wiki article.
I'm assuming as a Japanese she might know the reading better since she uses that word.

@@ -8 +8 @@
-<reb>はせん</reb>
+<reb>なみせん</reb>