I reported that bug to gentoo already 
http://bugs.gentoo.org/show_bug.cgi?id=58470

[snip]
dev-cpp/gtkmm-2.4.3 does not install any .so files. There are no shared object 
files with the common .so ending. The libtool .la file correctly states:
library_names='libgtkmm-2.4.1.0.3 libgtkmm-2.4.1 libgtkmm-2.4'


Reproducible: Always
Steps to Reproduce:
1. emerge dev-cpp/gtkmm
2. ls -al /usr/lib/libgtkmm*


Actual Results:  
-rwxr-xr-x  1 root root    1214 Jul 10 12:21 libgtkmm-2.0.la
lrwxrwxrwx  1 root root      22 Jun 24 18:38 libgtkmm-2.0.so -> libgtkmm-2.0.so.
1.5.11
lrwxrwxrwx  1 root root      22 Jun 24 18:38 libgtkmm-2.0.so.1 -> libgtkmm-2.0.
so.1.5.11
-rwxr-xr-x  1 root root 3669310 Jun 24 18:38 libgtkmm-2.0.so.1.5.11
lrwxrwxrwx  1 root root      18 Jul 26 23:26 libgtkmm-2.4 -> libgtkmm-2.4.1.0.3
lrwxrwxrwx  1 root root      18 Jul 26 23:26 libgtkmm-2.4.1 -> libgtkmm-2.4.1.0.
3
-rwxr-xr-x  1 root root 4328776 Jul 26 23:26 libgtkmm-2.4.1.0.3
-rwxr-xr-x  1 root root    1294 Jul 26 23:26 libgtkmm-2.4.la
-rwxr-xr-x  1 root root    1334 Jul 10 12:21 libgtkmm_generate_extra_defs-2.0.la
lrwxrwxrwx  1 root root      42 Jun 24 18:38 libgtkmm_generate_extra_defs-2.0.so 
-> libgtkmm_generate_extra_defs-2.0.so.1.5.11
lrwxrwxrwx  1 root root      42 Jun 24 18:38 libgtkmm_generate_extra_defs-2.0.
so.1 -> libgtkmm_generate_extra_defs-2.0.so.1.5.11

Expected Results:  
I expected some libgtkmm-2.4.so files. 
[snap]

From a gentoo-dev i got the input that this behaviour only occurs with libtool-
1.5.6. I have version 1.5.2 installed here. But the script files in the package 
are from 1.5.6. I do not know how libtool interacts.. and whether the installed 
version plays a role at all. 

To fix that issue I run libtoolize --force before configure starts, then 
everything works fine