I'd see the opportunity for three things to happen here:
1 - You show knowledge about the craft - you are able to articulately (and concisely!) explain the problem and a potential solution
2 - You show good communication and tact - you are able provide negative feedback without being a jerk.
3 - You get for yourself a sense of what sort of team you'll be working on and whether you'll be happy - My experience has been that most smart/talented people do not enjoy working unskilled/undedicated people - people admire diligence in each other, it's a big motivator - so if this team isn't interested in doing good work, you may hate the job.
Items 1 & 2 are about getting a job, Item 3 is about deciding whether you WANT the job.
First - ask
Start with something tactful - "I'm interested in these design choices", "this is a different style than I'm used to, could you explain the rationale for doing it this way?". Something non-judgmental and very open ended. You've heard it was their top person - my initial reaction would be to assume that if this site is really horrendous, they don't know any better. I'd say it's a rare case where they are deliberately lying to you to see if you'll call their bluff. Particularly in engineering - these kind of skills are not a major part of the skill set required.
Watch the reaction
Watch the reaction - if the initial prods are met with defensiveness or willful blindness, you have two options:
- Offer critique - "Do you mind some thoughts? I have a lot of experience here"
- Shut up - Decide it's not worth the risk. It's your call - I don't know how desperate, or eager you are for this job. And no one else is standing in your shoes to judge whether the reaction is truly defensive or just reserved.
Proceed with caution - offering critique is never easy, and you're not an insider yet. People have to want your advice to take it.
Keep it short
When offering critique, it's easy to rant. Keep yourself short and sweet. Summarize, don't offer long explanations that may not be warranted. Suppose you are talking to an equal and let them guide you with questions if they don't understand. While explaining anything truly esoteric, unasked, is helpful - explaining anything that should be standard to best practices (even if it does not to be something they appear to understand, given the example at hand) can come off as condescending.
It's also good to be respectful of time limits. Most interviews have a narrow window - managers do a LOT of interviews in a thriving team, and they have to balance this in with a lot of other time demands. If you don't keep the ideas short and sweet, you risk the opportunity to respond to other questions or concerns that are important to determine suitability for the position.
Focus on the "What to do"
It's easy to point out glaring mistakes. It's definitely more challenging but better politics to focus on the good things to try. It's much easier to say "This site would really shine if you did XYZ - here's why it would be awesome... (more maintainable, more attractive, cheaper, etc)" and sound like a supportive team member. Saying "This site as it is is an example of poor skills in the following ways... as it is it's (expensive, hard to maintain, ugly)" is usually going to raise defensiveness.
Getting from the "don't do" to the "please do" isn't always easy. I've been awfully vague in the process of trying to put things this way, but it's generally a good way to start a discussion.
You're interviewing them, too
Hopefully you're talking to a potential manager or team member. If you don't get the reaction that you'd want on the job - consider that. People are unlikely to change their character - if you think the person is defensive, hostile or disinterested, and this is something you care deeply about -- do you really want to work here?