I also checked how other implementations deal with invalid DER encoding. NSS 3.41, Firefox, and Chromium accept the certifiate.

NSS shows the serial number as "102 (0x66)"
Firefox and Chromium display the serial number as "00:00:00:66".

$ echo "password" > passwd
$ certutil -d . -f passwd -N
$ certutil -d . -f passwd -A -n ca -i ../ca.pem -t C,C,C
$ certutil -d . -L -n ca
Certificate:
    Data:
        Version: 3 (0x2)
        Serial Number: 102 (0x66)
        Signature Algorithm: PKCS #1 SHA-1 With RSA Encryption
        Issuer: "C=RS,L=Beograd,O=MUP Republike Srbije,CN=MUPCA Root"
        Validity:
            Not Before: Sat Feb 27 16:19:18 2010
            Not After : Thu Feb 27 16:19:18 2020
        Subject: "C=Re...,L=Beograd,O=MUP Republike Srbije,CN=MUPCA Resursi"
        Subject Public Key Info:
            Public Key Algorithm: PKCS #1 RSA Encryption
            RSA Public Key:
                Modulus:
                    ea:69:46:bc:c7:70:00:d5:f5:32:8d:c7:4e:ad:3a:a5:
                    d3:29:7e:a2:46:12:a9:dd:57:75:b1:49:95:80:20:ed:
                    9b:68:6b:e3:c5:55:d8:64:15:68:42:ab:a3:f7:c0:96:
                    37:08:51:cb:05:ca:b5:99:f6:07:a6:8b:f2:cd:d2:f5:
                    d6:16:12:da:bf:a8:0b:9c:45:5d:ac:79:1d:a8:67:47:
                    ee:7f:83:40:f8:58:00:d5:dd:c4:c9:52:1b:d2:f4:ce:
                    e1:fa:8a:66:d3:18:86:1e:ea:fc:0a:8b:b5:ec:49:cd:
                    86:bf:8b:7e:b0:61:81:ec:ea:99:4f:64:82:96:93:9d:
                    ab:80:7d:a7:27:65:00:d4:12:26:98:45:64:7e:76:0b:
                    98:ff:16:50:49:0c:45:20:82:ce:2e:23:a2:65:3a:b7:
                    44:cd:51:00:d9:bf:e3:1f:de:23:1d:57:e9:32:c3:55:
                    f0:24:af:d4:cf:cd:9e:77:1f:19:7e:1c:03:5b:7a:e4:
                    75:84:3b:d4:1d:e9:23:d6:8c:f2:8f:b2:0d:e3:79:df:
                    9e:03:1e:0e:15:5b:7b:0c:dd:6e:4d:82:86:5a:63:79:
                    64:b5:07:79:dd:fd:08:e3:d6:cb:60:01:fd:82:11:59:
                    2c:8d:22:f8:f9:91:59:b1:cd:12:7b:39:6d:08:82:5d
                Exponent: 65537 (0x10001)
        Signed Extensions:
            Name: Certificate Basic Constraints
            Critical: True
            Data: Is a CA with no maximum path length.

            Name: Certificate Key Usage
            Critical: True
            Usages: Certificate Signing
                    CRL Signing

            Name: Authority Information Access
            Method: PKIX CA issuers access method
            Location: 
                URI: "http://ca.mup.gov.rs/MUPCARoot.crt"

            Name: Certificate Subject Key ID
            Data:
                cb:f9:00:a9:b7:b6:c1:6f:44:43:d0:22:ad:fc:0e:6e:
                cc:8f:f6:0f

            Name: Certificate Authority Key Identifier
            Key ID:
                3f:66:b0:0f:66:fb:f0:10:2e:61:a4:6f:ef:2c:95:8a:
                14:72:6f:71

            Name: CRL Distribution Points
            Distribution point:
                URI: "http://ca.mup.gov.rs/MUPCARoot.crl"

    Signature Algorithm: PKCS #1 SHA-1 With RSA Encryption